Starting phenix.real_space_refine
on Wed Mar 12 00:07:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c7u_45294/03_2025/9c7u_45294_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c7u_45294/03_2025/9c7u_45294.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c7u_45294/03_2025/9c7u_45294.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c7u_45294/03_2025/9c7u_45294.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c7u_45294/03_2025/9c7u_45294_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c7u_45294/03_2025/9c7u_45294_neut.cif"
  }
  resolution = 3.65
  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=   0.012
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: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    4356      2.51       5
     N    1189      2.21       5
     O    1276      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6848
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3979
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 3979
          Classifications: {'peptide': 505}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 17, 'TRANS': 487}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 1482
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 186, 1482
          Classifications: {'peptide': 186}
          Link IDs: {'PTRANS': 10, 'TRANS': 175}
    Chain: "C"
      Number of atoms: 1373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 1373
          Classifications: {'peptide': 205}
          Incomplete info: {'truncation_to_alanine': 69}
          Link IDs: {'PTRANS': 3, 'TRANS': 201}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 263
          Unresolved non-hydrogen angles: 338
          Unresolved non-hydrogen dihedrals: 226
          Unresolved non-hydrogen chiralities: 28
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 9, 'GLU:plan': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 137
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.64, per 1000 atoms: 0.82
  Number of scatterers: 6848
  At special positions: 0
  Unit cell: (61.568, 79.872, 160.576, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      27     16.00
     O    1276      8.00
     N    1189      7.00
     C    4356      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 692 " - pdb=" SG  CYS B 716 " distance=2.03

  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
  Links applied
    NAG-ASN
      " NAG A 601 " - " ASN A 428 "
  Time building additional restraints: 1.83
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1692

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 7 sheets defined
      45.5% alpha, 10.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 90 through 92
      No H-bonds generated for 'chain 'A' and resid 90 through 92'
    Processing helix  chain 'A' and resid 93 through 103
    Processing helix  chain 'A' and resid 120 through 136
      removed outlier: 3.637A  pdb=" N   GLU A 131 " --> pdb=" O   PHE A 127 " (cutoff:3.500A)
      Proline residue:  A 132  - end of helix
    Processing helix  chain 'A' and resid 149 through 165
      removed outlier: 3.591A  pdb=" N   ALA A 164 " --> pdb=" O   GLN A 160 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   SER A 165 " --> pdb=" O   ALA A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 180
    Processing helix  chain 'A' and resid 231 through 235
    Processing helix  chain 'A' and resid 241 through 261
      removed outlier: 3.809A  pdb=" N   SER A 246 " --> pdb=" O   GLY A 242 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   VAL A 247 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   TYR A 261 " --> pdb=" O   ARG A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 265
    Processing helix  chain 'A' and resid 282 through 292
    Processing helix  chain 'A' and resid 332 through 348
    Processing helix  chain 'A' and resid 371 through 378
      removed outlier: 4.031A  pdb=" N   PHE A 375 " --> pdb=" O   GLU A 371 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ARG A 378 " --> pdb=" O   ARG A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 406
    Processing helix  chain 'A' and resid 407 through 427
    Processing helix  chain 'A' and resid 429 through 433
      removed outlier: 4.044A  pdb=" N   GLY A 433 " --> pdb=" O   THR A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 462
      removed outlier: 4.233A  pdb=" N   GLN A 462 " --> pdb=" O   TRP A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 485
    Processing helix  chain 'A' and resid 521 through 553
      removed outlier: 3.747A  pdb=" N   ASP A 525 " --> pdb=" O   PRO A 521 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   VAL A 543 " --> pdb=" O   ALA A 539 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   GLN A 544 " --> pdb=" O   TYR A 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 689 through 695
      removed outlier: 4.138A  pdb=" N   ILE B 694 " --> pdb=" O   ASP B 691 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 773 through 775
      No H-bonds generated for 'chain 'B' and resid 773 through 775'
    Processing helix  chain 'C' and resid 3 through 24
      removed outlier: 3.837A  pdb=" N   PHE C  15 " --> pdb=" O   ALA C  11 " (cutoff:3.500A)
      Proline residue:  C  16  - end of helix
    Processing helix  chain 'C' and resid 25 through 29
    Processing helix  chain 'C' and resid 31 through 56
    Processing helix  chain 'C' and resid 69 through 91
      removed outlier: 3.860A  pdb=" N   ASN C  91 " --> pdb=" O   VAL C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 94 through 113
      removed outlier: 3.760A  pdb=" N   GLY C 105 " --> pdb=" O   VAL C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 116 through 122
    Processing helix  chain 'C' and resid 130 through 157
      removed outlier: 3.522A  pdb=" N   LEU C 143 " --> pdb=" O   SER C 139 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   VAL C 144 " --> pdb=" O   ASN C 140 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 177
    Processing helix  chain 'C' and resid 178 through 190
    Processing helix  chain 'C' and resid 194 through 220
    Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 47
      removed outlier: 3.538A  pdb=" N   HIS A  44 " --> pdb=" O   ALA A 516 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   THR A  70 " --> pdb=" O   MET A 186 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 50
      removed outlier: 6.229A  pdb=" N   VAL A 108 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
      removed outlier: 7.412A  pdb=" N   ALA A 146 " --> pdb=" O   VAL A 108 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   ILE A 110 " --> pdb=" O   ALA A 146 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56
    Processing sheet with id=AA4, first strand: chain 'A' and resid 353 through 358
      removed outlier: 3.768A  pdb=" N   SER A 355 " --> pdb=" O   LEU A 320 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU A 322 " --> pdb=" O   SER A 355 " (cutoff:3.500A)
      removed outlier: 5.807A  pdb=" N   VAL A 308 " --> pdb=" O   PHE A 383 " (cutoff:3.500A)
      removed outlier: 7.261A  pdb=" N   LEU A 385 " --> pdb=" O   VAL A 308 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   CYS A 310 " --> pdb=" O   LEU A 385 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   LEU A 309 " --> pdb=" O   THR A 218 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   VAL A 220 " --> pdb=" O   LEU A 309 " (cutoff:3.500A)
      removed outlier: 7.710A  pdb=" N   LEU A 311 " --> pdb=" O   VAL A 220 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   VAL A 222 " --> pdb=" O   LEU A 311 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   ILE A 219 " --> pdb=" O   LEU A 271 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   PHE A 273 " --> pdb=" O   ILE A 219 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   ILE A 221 " --> pdb=" O   PHE A 273 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   SER A 275 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   ILE A 201 " --> pdb=" O   HIS A 494 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   HIS A 494 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
      removed outlier: 5.851A  pdb=" N   SER A 203 " --> pdb=" O   GLN A 492 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   GLN A 492 " --> pdb=" O   SER A 203 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   GLU A 205 " --> pdb=" O   VAL A 490 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   VAL A 490 " --> pdb=" O   GLU A 205 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 669 through 672
      removed outlier: 6.558A  pdb=" N   THR B 670 " --> pdb=" O   ILE B 752 " (cutoff:3.500A)
      removed outlier: 7.850A  pdb=" N   VAL B 754 " --> pdb=" O   THR B 670 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   SER B 672 " --> pdb=" O   VAL B 754 " (cutoff:3.500A)
      removed outlier: 8.504A  pdb=" N   ARG B 756 " --> pdb=" O   SER B 672 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 698 through 700
      removed outlier: 3.919A  pdb=" N   GLU B 685 " --> pdb=" O   GLN B 721 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   TYR B 718 " --> pdb=" O   ILE B 740 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ILE B 740 " --> pdb=" O   TYR B 718 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   VAL B 720 " --> pdb=" O   ARG B 738 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ARG B 738 " --> pdb=" O   VAL B 720 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 777 through 779

    311 hydrogen bonds defined for protein.
    888 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: 1.95

  Time building geometry restraints manager: 2.11 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2282
        1.34 -     1.46: 1383
        1.46 -     1.58: 3276
        1.58 -     1.69: 0
        1.69 -     1.81: 47
  Bond restraints: 6988
  Sorted by residual:
  bond pdb=" C5  NAG A 601 "
       pdb=" O5  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.23e+00
  bond pdb=" N   ASP A 525 "
       pdb=" CA  ASP A 525 "
    ideal  model  delta    sigma   weight residual
    1.458  1.445  0.013 1.30e-02 5.92e+03 9.55e-01
  bond pdb=" C3  NAG A 601 "
       pdb=" O3  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.403  1.422 -0.019 2.00e-02 2.50e+03 9.36e-01
  bond pdb=" CA  GLU A 431 "
       pdb=" CB  GLU A 431 "
    ideal  model  delta    sigma   weight residual
    1.524  1.538 -0.014 1.51e-02 4.39e+03 8.76e-01
  bond pdb=" CB  ILE A 155 "
       pdb=" CG2 ILE A 155 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.37e-01
  ... (remaining 6983 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 9342
        1.93 -     3.86: 137
        3.86 -     5.80: 19
        5.80 -     7.73: 6
        7.73 -     9.66: 3
  Bond angle restraints: 9507
  Sorted by residual:
  angle pdb=" CA  GLU A 431 "
        pdb=" CB  GLU A 431 "
        pdb=" CG  GLU A 431 "
      ideal   model   delta    sigma   weight residual
     114.10  122.25   -8.15 2.00e+00 2.50e-01 1.66e+01
  angle pdb=" CB  MET A 456 "
        pdb=" CG  MET A 456 "
        pdb=" SD  MET A 456 "
      ideal   model   delta    sigma   weight residual
     112.70  122.36   -9.66 3.00e+00 1.11e-01 1.04e+01
  angle pdb=" CB  ARG A 339 "
        pdb=" CG  ARG A 339 "
        pdb=" CD  ARG A 339 "
      ideal   model   delta    sigma   weight residual
     111.30  117.24   -5.94 2.30e+00 1.89e-01 6.66e+00
  angle pdb=" N   PHE C   4 "
        pdb=" CA  PHE C   4 "
        pdb=" C   PHE C   4 "
      ideal   model   delta    sigma   weight residual
     112.54  109.44    3.10 1.22e+00 6.72e-01 6.44e+00
  angle pdb=" C   GLU A 431 "
        pdb=" CA  GLU A 431 "
        pdb=" CB  GLU A 431 "
      ideal   model   delta    sigma   weight residual
     111.40  114.64   -3.24 1.29e+00 6.01e-01 6.31e+00
  ... (remaining 9502 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 3563
       17.86 -    35.71: 457
       35.71 -    53.57: 114
       53.57 -    71.43: 22
       71.43 -    89.28: 5
  Dihedral angle restraints: 4161
    sinusoidal: 1545
      harmonic: 2616
  Sorted by residual:
  dihedral pdb=" CA  SER A 397 "
           pdb=" C   SER A 397 "
           pdb=" N   SER A 398 "
           pdb=" CA  SER A 398 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.66   21.34     0      5.00e+00 4.00e-02 1.82e+01
  dihedral pdb=" CA  ILE A 130 "
           pdb=" C   ILE A 130 "
           pdb=" N   GLU A 131 "
           pdb=" CA  GLU A 131 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.12  -18.88     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  THR A  74 "
           pdb=" C   THR A  74 "
           pdb=" N   MET A  75 "
           pdb=" CA  MET A  75 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.41  -18.59     0      5.00e+00 4.00e-02 1.38e+01
  ... (remaining 4158 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 862
       0.046 -    0.092: 180
       0.092 -    0.138: 53
       0.138 -    0.184: 0
       0.184 -    0.230: 1
  Chirality restraints: 1096
  Sorted by residual:
  chirality pdb=" C1  NAG A 601 "
            pdb=" ND2 ASN A 428 "
            pdb=" C2  NAG A 601 "
            pdb=" O5  NAG A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CA  THR A 313 "
            pdb=" N   THR A 313 "
            pdb=" C   THR A 313 "
            pdb=" CB  THR A 313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.13 2.00e-01 2.50e+01 4.00e-01
  chirality pdb=" CA  VAL B 815 "
            pdb=" N   VAL B 815 "
            pdb=" C   VAL B 815 "
            pdb=" CB  VAL B 815 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.98e-01
  ... (remaining 1093 not shown)

  Planarity restraints: 1228
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C   4 "   -0.018 2.00e-02 2.50e+03   1.86e-02 6.06e+00
        pdb=" CG  PHE C   4 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 PHE C   4 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE C   4 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE C   4 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 PHE C   4 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE C   4 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 434 "    0.028 5.00e-02 4.00e+02   4.26e-02 2.90e+00
        pdb=" N   PRO A 435 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 435 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 435 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 778 "   -0.013 2.00e-02 2.50e+03   9.88e-03 2.44e+00
        pdb=" CG  TRP B 778 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 778 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 778 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 778 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 778 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 778 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 778 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 778 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 778 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1225 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 193
        2.69 -     3.24: 6982
        3.24 -     3.80: 10900
        3.80 -     4.35: 13433
        4.35 -     4.90: 22381
  Nonbonded interactions: 53889
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 258 "
            pdb=" OG1 THR A 264 "
     model   vdw
     2.138 3.040
  nonbonded pdb=" OG  SER A 256 "
            pdb=" O   TYR A 486 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" N   GLU C 127 "
            pdb=" OE1 GLU C 127 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" OD1 ASP A 525 "
            pdb=" ND2 ASN C   8 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" OD1 ASN B 813 "
            pdb=" OG1 THR B 837 "
     model   vdw
     2.264 3.040
  ... (remaining 53884 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:             5.200
  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:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.660
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
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   0.036   6988  Z= 0.219
  Angle     :  0.611   9.660   9507  Z= 0.325
  Chirality :  0.041   0.230   1096
  Planarity :  0.004   0.043   1227
  Dihedral  : 16.991  89.285   2466
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.18 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 33.28 %
    Favored  : 66.42 %
  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: -0.72 (0.30), residues: 882
  helix:  2.11 (0.27), residues: 367
  sheet: -2.40 (0.42), residues: 157
  loop : -2.42 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 778 
 HIS   0.005   0.001   HIS B 844 
 PHE   0.043   0.002   PHE C   4 
 TYR   0.020   0.001   TYR C 216 
 ARG   0.003   0.000   ARG A 464 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 106
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
REVERT: A  450 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7743 (pt0)
  outliers start: 2
  outliers final: 1
  residues processed: 108
  average time/residue: 0.1614
  time to fit residues: 24.7000
Evaluate side-chains
  102 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain B residue  792 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:   10.0000
   chunk 66 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0020
   chunk 68 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.9790

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

Flipped N/Q/H residues before XYZ refinement:
** A  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 302 GLN
** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   8 ASN ** 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 = 0.3891 r_free = 0.3891 target = 0.142906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.101963 restraints weight = 10435.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.105170 restraints weight = 5923.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.107173 restraints weight = 4192.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.0754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6988  Z= 0.317
  Angle     :  0.603   8.226   9507  Z= 0.314
  Chirality :  0.044   0.225   1096
  Planarity :  0.004   0.043   1227
  Dihedral  :  6.133  84.208    996
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.32 %
    Favored  : 89.68 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 28.20 %
    Favored  : 66.42 %
  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: -0.73 (0.30), residues: 882
  helix:  2.05 (0.27), residues: 362
  sheet: -2.29 (0.43), residues: 149
  loop : -2.38 (0.32), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 778 
 HIS   0.005   0.001   HIS B 844 
 PHE   0.015   0.002   PHE C   4 
 TYR   0.010   0.001   TYR C  29 
 ARG   0.002   0.000   ARG A 413 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 115
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
REVERT: A  456 MET cc_start: 0.8439 (mmm) cc_final: 0.8215 (mmm)
REVERT: B  731 GLU cc_start: 0.8466 (tm-30) cc_final: 0.7778 (tt0)
  outliers start: 37
  outliers final: 24
  residues processed: 141
  average time/residue: 0.1753
  time to fit residues: 34.3168
Evaluate side-chains
  123 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  397 SER
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain B residue  690 ASN
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  751 ASN
Chi-restraints excluded: chain B residue  807 LEU
Chi-restraints excluded: chain B residue  819 ASP
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  208 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 82 optimal weight:   10.0000
   chunk 61 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 52 optimal weight:    8.9990
   chunk 84 optimal weight:   10.0000
   chunk 63 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 689 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 = 0.3894 r_free = 0.3894 target = 0.143048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.105120 restraints weight = 10592.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.105644 restraints weight = 6916.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.107382 restraints weight = 4844.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.1060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6988  Z= 0.285
  Angle     :  0.588  10.917   9507  Z= 0.304
  Chirality :  0.043   0.216   1096
  Planarity :  0.004   0.042   1227
  Dihedral  :  4.977  40.910    990
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.43 %
    Favored  : 89.57 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 29.51 %
    Favored  : 64.83 %
  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: -0.81 (0.30), residues: 882
  helix:  2.01 (0.27), residues: 363
  sheet: -2.42 (0.41), residues: 152
  loop : -2.41 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 778 
 HIS   0.005   0.001   HIS B 844 
 PHE   0.010   0.002   PHE B 801 
 TYR   0.010   0.001   TYR A 261 
 ARG   0.002   0.000   ARG A  50 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 104
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 MET cc_start: 0.8011 (ttp) cc_final: 0.7740 (ttp)
REVERT: A  456 MET cc_start: 0.8424 (mmm) cc_final: 0.8156 (mmm)
REVERT: B  704 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8178 (pp20)
REVERT: C   21 TYR cc_start: 0.5864 (OUTLIER) cc_final: 0.5165 (t80)
  outliers start: 39
  outliers final: 26
  residues processed: 131
  average time/residue: 0.1652
  time to fit residues: 30.2556
Evaluate side-chains
  124 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  241 ASN
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  397 SER
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 MET
Chi-restraints excluded: chain B residue  684 MET
Chi-restraints excluded: chain B residue  704 GLU
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  751 ASN
Chi-restraints excluded: chain B residue  807 LEU
Chi-restraints excluded: chain B residue  813 ASN
Chi-restraints excluded: chain B residue  819 ASP
Chi-restraints excluded: chain C residue   21 TYR
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  208 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 57 optimal weight:    8.9990
   chunk 76 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 84 optimal weight:   20.0000
   chunk 30 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0980
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 134 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.142144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.101552 restraints weight = 10650.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.104732 restraints weight = 5943.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.106638 restraints weight = 4183.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.1247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6988  Z= 0.291
  Angle     :  0.592  11.231   9507  Z= 0.303
  Chirality :  0.043   0.210   1096
  Planarity :  0.004   0.042   1227
  Dihedral  :  4.801  27.168    990
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.43 %
    Favored  : 89.57 %
  Rotamer:
    Outliers :  7.27 %
    Allowed  : 29.51 %
    Favored  : 63.23 %
  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: -0.81 (0.30), residues: 882
  helix:  1.89 (0.27), residues: 368
  sheet: -2.34 (0.43), residues: 141
  loop : -2.39 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 778 
 HIS   0.005   0.001   HIS B 844 
 PHE   0.014   0.002   PHE B 836 
 TYR   0.013   0.001   TYR C  29 
 ARG   0.002   0.000   ARG A  82 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 103
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  456 MET cc_start: 0.8457 (mmm) cc_final: 0.8146 (mmm)
REVERT: C   21 TYR cc_start: 0.6124 (OUTLIER) cc_final: 0.5291 (t80)
  outliers start: 50
  outliers final: 39
  residues processed: 139
  average time/residue: 0.1599
  time to fit residues: 31.3274
Evaluate side-chains
  135 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 95
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  241 ASN
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  397 SER
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  739 VAL
Chi-restraints excluded: chain B residue  751 ASN
Chi-restraints excluded: chain B residue  792 GLN
Chi-restraints excluded: chain B residue  807 LEU
Chi-restraints excluded: chain B residue  813 ASN
Chi-restraints excluded: chain B residue  819 ASP
Chi-restraints excluded: chain C residue   21 TYR
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  208 LEU
Chi-restraints excluded: chain C residue  215 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 75 optimal weight:    5.9990
   chunk 6 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0060
   chunk 27 optimal weight:    0.0010
   overall best weight:    0.5404

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

Flipped N/Q/H residues before XYZ refinement:
A  44 HIS
A  59 GLN
** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 134 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.143783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.103485 restraints weight = 10491.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.106726 restraints weight = 5915.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.108798 restraints weight = 4155.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.1336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6988  Z= 0.205
  Angle     :  0.538   6.959   9507  Z= 0.280
  Chirality :  0.042   0.201   1096
  Planarity :  0.004   0.041   1227
  Dihedral  :  4.605  20.941    990
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.75 %
    Favored  : 90.25 %
  Rotamer:
    Outliers :  7.41 %
    Allowed  : 28.92 %
    Favored  : 63.66 %
  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: -0.73 (0.30), residues: 882
  helix:  1.97 (0.27), residues: 368
  sheet: -2.40 (0.41), residues: 153
  loop : -2.29 (0.33), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 778 
 HIS   0.006   0.001   HIS B 844 
 PHE   0.012   0.001   PHE B 836 
 TYR   0.009   0.001   TYR A 486 
 ARG   0.002   0.000   ARG A 114 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 106
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  356 MET cc_start: 0.7947 (ttp) cc_final: 0.7718 (ttp)
REVERT: A  456 MET cc_start: 0.8357 (mmm) cc_final: 0.8086 (mmm)
REVERT: B  786 ASN cc_start: 0.7361 (OUTLIER) cc_final: 0.6657 (p0)
REVERT: C   21 TYR cc_start: 0.6170 (OUTLIER) cc_final: 0.5294 (t80)
REVERT: C  115 ARG cc_start: 0.7421 (mtt90) cc_final: 0.7123 (mtt90)
  outliers start: 51
  outliers final: 34
  residues processed: 143
  average time/residue: 0.1464
  time to fit residues: 30.2419
Evaluate side-chains
  138 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 102
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  397 SER
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  739 VAL
Chi-restraints excluded: chain B residue  751 ASN
Chi-restraints excluded: chain B residue  786 ASN
Chi-restraints excluded: chain B residue  792 GLN
Chi-restraints excluded: chain B residue  807 LEU
Chi-restraints excluded: chain B residue  812 GLU
Chi-restraints excluded: chain B residue  813 ASN
Chi-restraints excluded: chain B residue  819 ASP
Chi-restraints excluded: chain C residue   21 TYR
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  208 LEU
Chi-restraints excluded: chain C residue  211 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 43 optimal weight:    0.0980
   chunk 82 optimal weight:    9.9990
   chunk 3 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 87 optimal weight:    8.9990
   chunk 77 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 134 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.143689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.106020 restraints weight = 10645.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.106939 restraints weight = 6688.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.108713 restraints weight = 4860.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.1445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6988  Z= 0.234
  Angle     :  0.552  10.372   9507  Z= 0.286
  Chirality :  0.042   0.194   1096
  Planarity :  0.004   0.040   1227
  Dihedral  :  4.579  20.838    990
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.86 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  7.70 %
    Allowed  : 28.63 %
    Favored  : 63.66 %
  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: -0.68 (0.30), residues: 882
  helix:  1.99 (0.27), residues: 368
  sheet: -2.28 (0.43), residues: 143
  loop : -2.31 (0.32), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 778 
 HIS   0.005   0.001   HIS B 844 
 PHE   0.040   0.002   PHE B 836 
 TYR   0.013   0.001   TYR A 261 
 ARG   0.001   0.000   ARG A  50 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 107
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 MET cc_start: 0.8018 (ttp) cc_final: 0.7754 (ttp)
REVERT: A  456 MET cc_start: 0.8449 (mmm) cc_final: 0.8142 (mmm)
REVERT: B  786 ASN cc_start: 0.7349 (OUTLIER) cc_final: 0.6921 (p0)
REVERT: C   21 TYR cc_start: 0.6207 (OUTLIER) cc_final: 0.5278 (t80)
REVERT: C  115 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6980 (tpp80)
  outliers start: 53
  outliers final: 41
  residues processed: 145
  average time/residue: 0.1454
  time to fit residues: 30.1768
Evaluate side-chains
  143 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 99
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  241 ASN
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  397 SER
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain B residue  684 MET
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  739 VAL
Chi-restraints excluded: chain B residue  751 ASN
Chi-restraints excluded: chain B residue  763 LEU
Chi-restraints excluded: chain B residue  786 ASN
Chi-restraints excluded: chain B residue  792 GLN
Chi-restraints excluded: chain B residue  807 LEU
Chi-restraints excluded: chain B residue  812 GLU
Chi-restraints excluded: chain B residue  813 ASN
Chi-restraints excluded: chain B residue  819 ASP
Chi-restraints excluded: chain B residue  846 THR
Chi-restraints excluded: chain C residue   21 TYR
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  115 ARG
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  208 LEU
Chi-restraints excluded: chain C residue  215 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 80 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0980
   chunk 8 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   chunk 83 optimal weight:   10.0000
   chunk 54 optimal weight:    0.0770
   chunk 84 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
** A  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 449 GLN
** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 134 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.144899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.105871 restraints weight = 10529.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.108138 restraints weight = 6493.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.109487 restraints weight = 4698.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.1486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6988  Z= 0.198
  Angle     :  0.570  13.297   9507  Z= 0.293
  Chirality :  0.042   0.246   1096
  Planarity :  0.004   0.039   1227
  Dihedral  :  4.495  20.755    990
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.30 %
    Favored  : 90.70 %
  Rotamer:
    Outliers :  6.98 %
    Allowed  : 29.80 %
    Favored  : 63.23 %
  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: 882
  helix:  2.03 (0.27), residues: 369
  sheet: -2.20 (0.43), residues: 143
  loop : -2.30 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 778 
 HIS   0.007   0.001   HIS B 842 
 PHE   0.030   0.002   PHE B 836 
 TYR   0.011   0.001   TYR A 261 
 ARG   0.002   0.000   ARG A  50 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 111
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 MET cc_start: 0.7967 (ttp) cc_final: 0.7705 (ttp)
REVERT: A  456 MET cc_start: 0.8373 (mmm) cc_final: 0.8069 (mmm)
REVERT: B  731 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7991 (tt0)
REVERT: B  786 ASN cc_start: 0.7328 (OUTLIER) cc_final: 0.6886 (p0)
REVERT: C   21 TYR cc_start: 0.6132 (OUTLIER) cc_final: 0.5226 (t80)
REVERT: C  115 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6913 (tpp80)
  outliers start: 48
  outliers final: 38
  residues processed: 144
  average time/residue: 0.1473
  time to fit residues: 31.0818
Evaluate side-chains
  145 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 103
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  397 SER
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain B residue  684 MET
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  731 GLU
Chi-restraints excluded: chain B residue  739 VAL
Chi-restraints excluded: chain B residue  751 ASN
Chi-restraints excluded: chain B residue  763 LEU
Chi-restraints excluded: chain B residue  786 ASN
Chi-restraints excluded: chain B residue  792 GLN
Chi-restraints excluded: chain B residue  807 LEU
Chi-restraints excluded: chain B residue  812 GLU
Chi-restraints excluded: chain B residue  813 ASN
Chi-restraints excluded: chain B residue  846 THR
Chi-restraints excluded: chain C residue   21 TYR
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  115 ARG
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  208 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 75 optimal weight:    6.9990
   chunk 61 optimal weight:    0.1980
   chunk 3 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   chunk 27 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9980
   chunk 79 optimal weight:    0.0370
   chunk 82 optimal weight:    0.0870
   chunk 29 optimal weight:    0.9980
   chunk 83 optimal weight:    8.9990
   overall best weight:    0.3036

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

Flipped N/Q/H residues before XYZ refinement:
A  44 HIS
A 444 GLN
** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 134 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.146557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.108115 restraints weight = 10542.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.110121 restraints weight = 6796.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.111821 restraints weight = 4495.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.1647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6988  Z= 0.173
  Angle     :  0.566  13.299   9507  Z= 0.287
  Chirality :  0.042   0.222   1096
  Planarity :  0.004   0.037   1227
  Dihedral  :  4.360  20.555    990
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.41 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 31.10 %
    Favored  : 62.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.30), residues: 882
  helix:  2.18 (0.27), residues: 368
  sheet: -2.17 (0.42), residues: 151
  loop : -2.21 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 778 
 HIS   0.005   0.001   HIS B 844 
 PHE   0.028   0.002   PHE B 836 
 TYR   0.019   0.001   TYR C 216 
 ARG   0.002   0.000   ARG A 114 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 110
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  356 MET cc_start: 0.7798 (ttp) cc_final: 0.7560 (ttp)
REVERT: A  456 MET cc_start: 0.8366 (mmm) cc_final: 0.8100 (mmm)
REVERT: B  731 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8124 (tt0)
REVERT: B  749 ASP cc_start: 0.9135 (t0) cc_final: 0.8886 (t0)
REVERT: B  786 ASN cc_start: 0.7289 (OUTLIER) cc_final: 0.6603 (p0)
REVERT: B  812 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7020 (mm-30)
REVERT: C   21 TYR cc_start: 0.6194 (OUTLIER) cc_final: 0.5296 (t80)
  outliers start: 42
  outliers final: 33
  residues processed: 139
  average time/residue: 0.1490
  time to fit residues: 29.7153
Evaluate side-chains
  139 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 102
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  397 SER
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain B residue  684 MET
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  731 GLU
Chi-restraints excluded: chain B residue  739 VAL
Chi-restraints excluded: chain B residue  751 ASN
Chi-restraints excluded: chain B residue  763 LEU
Chi-restraints excluded: chain B residue  786 ASN
Chi-restraints excluded: chain B residue  792 GLN
Chi-restraints excluded: chain B residue  807 LEU
Chi-restraints excluded: chain B residue  812 GLU
Chi-restraints excluded: chain B residue  813 ASN
Chi-restraints excluded: chain B residue  819 ASP
Chi-restraints excluded: chain B residue  846 THR
Chi-restraints excluded: chain C residue   21 TYR
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  115 ARG
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  208 LEU
Chi-restraints excluded: chain C residue  215 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 12 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 72 optimal weight:    9.9990
   chunk 17 optimal weight:    0.8980
   chunk 28 optimal weight:    0.2980
   chunk 53 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 134 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.144667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.105549 restraints weight = 10702.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.108066 restraints weight = 6351.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.109025 restraints weight = 4530.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6988  Z= 0.262
  Angle     :  0.587   9.380   9507  Z= 0.303
  Chirality :  0.043   0.225   1096
  Planarity :  0.004   0.037   1227
  Dihedral  :  4.407  20.841    990
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.41 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 31.10 %
    Favored  : 62.65 %
  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: -0.59 (0.30), residues: 882
  helix:  2.10 (0.27), residues: 369
  sheet: -2.29 (0.41), residues: 152
  loop : -2.26 (0.33), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 778 
 HIS   0.005   0.001   HIS B 842 
 PHE   0.027   0.002   PHE B 836 
 TYR   0.018   0.001   TYR C 216 
 ARG   0.002   0.000   ARG A 339 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 108
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 MET cc_start: 0.7994 (ttp) cc_final: 0.7686 (ttp)
REVERT: A  456 MET cc_start: 0.8509 (mmm) cc_final: 0.8171 (mmm)
REVERT: B  731 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8144 (tt0)
REVERT: B  786 ASN cc_start: 0.7335 (OUTLIER) cc_final: 0.6876 (p0)
REVERT: B  812 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7034 (mm-30)
REVERT: C   21 TYR cc_start: 0.6265 (OUTLIER) cc_final: 0.5390 (t80)
  outliers start: 43
  outliers final: 34
  residues processed: 136
  average time/residue: 0.1549
  time to fit residues: 30.0557
Evaluate side-chains
  143 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 105
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  241 ASN
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  397 SER
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain B residue  684 MET
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  731 GLU
Chi-restraints excluded: chain B residue  739 VAL
Chi-restraints excluded: chain B residue  751 ASN
Chi-restraints excluded: chain B residue  786 ASN
Chi-restraints excluded: chain B residue  792 GLN
Chi-restraints excluded: chain B residue  807 LEU
Chi-restraints excluded: chain B residue  812 GLU
Chi-restraints excluded: chain B residue  813 ASN
Chi-restraints excluded: chain B residue  846 THR
Chi-restraints excluded: chain C residue   21 TYR
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  208 LEU
Chi-restraints excluded: chain C residue  215 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 18 optimal weight:    0.3980
   chunk 33 optimal weight:    0.6980
   chunk 49 optimal weight:    6.9990
   chunk 26 optimal weight:    0.5980
   chunk 82 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 134 GLN
C 152 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.144643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.105885 restraints weight = 10817.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.109256 restraints weight = 6425.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.110146 restraints weight = 4082.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6988  Z= 0.239
  Angle     :  0.591   9.764   9507  Z= 0.304
  Chirality :  0.043   0.225   1096
  Planarity :  0.005   0.091   1227
  Dihedral  :  4.428  20.766    990
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 31.98 %
    Favored  : 62.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.61 (0.30), residues: 882
  helix:  2.09 (0.27), residues: 368
  sheet: -2.28 (0.42), residues: 152
  loop : -2.27 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 778 
 HIS   0.007   0.001   HIS B 842 
 PHE   0.030   0.002   PHE B 836 
 TYR   0.019   0.001   TYR C 216 
 ARG   0.008   0.000   ARG A 114 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 108
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 MET cc_start: 0.8006 (ttp) cc_final: 0.7706 (ttp)
REVERT: A  456 MET cc_start: 0.8501 (mmm) cc_final: 0.8208 (mmm)
REVERT: B  731 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8087 (tt0)
REVERT: B  749 ASP cc_start: 0.9141 (t0) cc_final: 0.8923 (t0)
REVERT: B  786 ASN cc_start: 0.7201 (OUTLIER) cc_final: 0.6760 (p0)
REVERT: B  812 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7050 (mm-30)
REVERT: C   21 TYR cc_start: 0.6254 (OUTLIER) cc_final: 0.5360 (t80)
  outliers start: 40
  outliers final: 33
  residues processed: 137
  average time/residue: 0.1686
  time to fit residues: 32.2952
Evaluate side-chains
  141 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 104
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  397 SER
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain B residue  684 MET
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  731 GLU
Chi-restraints excluded: chain B residue  739 VAL
Chi-restraints excluded: chain B residue  786 ASN
Chi-restraints excluded: chain B residue  792 GLN
Chi-restraints excluded: chain B residue  807 LEU
Chi-restraints excluded: chain B residue  812 GLU
Chi-restraints excluded: chain B residue  813 ASN
Chi-restraints excluded: chain B residue  846 THR
Chi-restraints excluded: chain C residue   21 TYR
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  208 LEU
Chi-restraints excluded: chain C residue  215 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 30 optimal weight:    0.1980
   chunk 65 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0570
   chunk 73 optimal weight:    7.9990
   chunk 76 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
** A  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 134 GLN
** C 152 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 = 0.3918 r_free = 0.3918 target = 0.144945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.106674 restraints weight = 10616.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.108953 restraints weight = 6360.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.110442 restraints weight = 4395.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6988  Z= 0.226
  Angle     :  0.598  10.793   9507  Z= 0.307
  Chirality :  0.043   0.228   1096
  Planarity :  0.004   0.038   1227
  Dihedral  :  4.385  20.720    990
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.64 %
    Favored  : 90.36 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 31.98 %
    Favored  : 62.35 %
  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: -0.60 (0.30), residues: 882
  helix:  2.05 (0.27), residues: 370
  sheet: -2.25 (0.42), residues: 152
  loop : -2.25 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 778 
 HIS   0.006   0.001   HIS B 842 
 PHE   0.029   0.002   PHE B 836 
 TYR   0.019   0.001   TYR C 216 
 ARG   0.007   0.000   ARG A 114 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2533.37 seconds
wall clock time: 44 minutes 33.12 seconds (2673.12 seconds total)