Starting phenix.real_space_refine
on Wed Feb 12 02:26:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9chx_45604/02_2025/9chx_45604.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9chx_45604/02_2025/9chx_45604.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9chx_45604/02_2025/9chx_45604.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9chx_45604/02_2025/9chx_45604.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9chx_45604/02_2025/9chx_45604.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9chx_45604/02_2025/9chx_45604.cif"
  }
  resolution = 3.5
  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=   0.010 sd=   0.075
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      48      5.16       5
     C    4644      2.51       5
     N    1164      2.21       5
     O    1273      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7129
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3450
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 432, 3450
          Classifications: {'peptide': 432}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 9, 'TRANS': 422}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "B"
      Number of atoms: 2792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 350, 2792
          Classifications: {'peptide': 350}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 20, 'TRANS': 329}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 41
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 44
    Chain: "C"
      Number of atoms: 808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 808
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 7, 'TRANS': 99}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'GLU%COO:oxt': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "A"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Unusual residues: {'CAU': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 57
          Unusual residues: {'FK5': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.96, per 1000 atoms: 0.70
  Number of scatterers: 7129
  At special positions: 0
  Unit cell: (68.85, 84.15, 155.55, 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      48     16.00
     O    1273      8.00
     N    1164      7.00
     C    4644      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 106 " - pdb=" SG  CYS A 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 184 " - pdb=" SG  CYS A 190 " 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
  Time building additional restraints: 1.85
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1668

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 4 sheets defined
      54.6% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 60
      removed outlier: 3.581A  pdb=" N   ILE A  58 " --> pdb=" O   VAL A  54 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LYS A  60 " --> pdb=" O   THR A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 97
      Proline residue:  A  88  - end of helix
    Processing helix  chain 'A' and resid 103 through 137
      removed outlier: 3.907A  pdb=" N   GLU A 107 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   THR A 123 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LEU A 124 " --> pdb=" O   SER A 120 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ILE A 135 " --> pdb=" O   ARG A 131 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   SER A 137 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 145
    Processing helix  chain 'A' and resid 146 through 171
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 178 through 186
    Processing helix  chain 'A' and resid 196 through 208
    Processing helix  chain 'A' and resid 209 through 226
    Processing helix  chain 'A' and resid 228 through 232
      removed outlier: 3.801A  pdb=" N   ALA A 232 " --> pdb=" O   GLN A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 246
    Processing helix  chain 'A' and resid 254 through 259
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 286 through 295
      removed outlier: 3.882A  pdb=" N   ILE A 291 " --> pdb=" O   PHE A 287 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   GLU A 292 " --> pdb=" O   LYS A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 315
      removed outlier: 3.928A  pdb=" N   LYS A 306 " --> pdb=" O   ASP A 302 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   TYR A 314 " --> pdb=" O   ALA A 310 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ASP A 315 " --> pdb=" O   PHE A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 336
      removed outlier: 3.791A  pdb=" N   LEU A 331 " --> pdb=" O   LEU A 327 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   MET A 334 " --> pdb=" O   VAL A 330 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLY A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 356
    Processing helix  chain 'A' and resid 364 through 372
    Processing helix  chain 'A' and resid 394 through 421
      Proline residue:  A 411  - end of helix
    Processing helix  chain 'A' and resid 429 through 444
      removed outlier: 4.127A  pdb=" N   ASN A 435 " --> pdb=" O   TYR A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 450
      removed outlier: 3.520A  pdb=" N   ILE A 448 " --> pdb=" O   PHE A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 463
      removed outlier: 3.800A  pdb=" N   ILE A 457 " --> pdb=" O   PRO A 453 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ALA A 458 " --> pdb=" O   ASP A 454 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   LEU A 462 " --> pdb=" O   ALA A 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 50
    Processing helix  chain 'B' and resid 56 through 73
      removed outlier: 4.028A  pdb=" N   GLN B  73 " --> pdb=" O   SER B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 105
    Processing helix  chain 'B' and resid 124 through 139
    Processing helix  chain 'B' and resid 152 through 159
      removed outlier: 3.577A  pdb=" N   THR B 156 " --> pdb=" O   CYS B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 169
    Processing helix  chain 'B' and resid 170 through 182
      removed outlier: 3.695A  pdb=" N   TYR B 174 " --> pdb=" O   SER B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 212
    Processing helix  chain 'B' and resid 224 through 230
      removed outlier: 3.709A  pdb=" N   LEU B 230 " --> pdb=" O   MET B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 271
    Processing helix  chain 'B' and resid 309 through 313
    Processing helix  chain 'B' and resid 342 through 346
      removed outlier: 3.779A  pdb=" N   MET B 346 " --> pdb=" O   PRO B 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 353
    Processing helix  chain 'B' and resid 353 through 369
      removed outlier: 3.514A  pdb=" N   GLU B 358 " --> pdb=" O   PRO B 354 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   LYS B 359 " --> pdb=" O   PHE B 355 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 56 through 64
      removed outlier: 3.965A  pdb=" N   ALA C  64 " --> pdb=" O   GLU C  60 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 79 through 80
      removed outlier: 3.502A  pdb=" N   ILE B  80 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   ILE B 276 " --> pdb=" O   ILE B 302 " (cutoff:3.500A)
      removed outlier: 7.906A  pdb=" N   ILE B 304 " --> pdb=" O   ILE B 276 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   ARG B 278 " --> pdb=" O   ILE B 304 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 143 through 145
    Processing sheet with id=AA3, first strand: chain 'C' and resid 4 through 8
      removed outlier: 6.984A  pdb=" N   VAL C   4 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 7.971A  pdb=" N   THR C  75 " --> pdb=" O   VAL C   4 " (cutoff:3.500A)
      removed outlier: 5.506A  pdb=" N   THR C   6 " --> pdb=" O   LYS C  73 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   LYS C  73 " --> pdb=" O   THR C   6 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   VAL C  98 " --> pdb=" O   MET C  29 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 49
      removed outlier: 6.237A  pdb=" N   HIS C  25 " --> pdb=" O   LEU C 103 " (cutoff:3.500A)
      removed outlier: 5.457A  pdb=" N   LEU C 103 " --> pdb=" O   HIS C  25 " (cutoff:3.500A)

    340 hydrogen bonds defined for protein.
    978 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: 1.92

  Time building geometry restraints manager: 2.10 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2232
        1.34 -     1.46: 1723
        1.46 -     1.58: 3277
        1.58 -     1.70: 0
        1.70 -     1.82: 73
  Bond restraints: 7305
  Sorted by residual:
  bond pdb=" C13 CAU A 501 "
       pdb=" O14 CAU A 501 "
    ideal  model  delta    sigma   weight residual
    1.342  1.399 -0.057 2.00e-02 2.50e+03 8.18e+00
  bond pdb=" N   SER A 203 "
       pdb=" CA  SER A 203 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.21e-02 6.83e+03 4.83e+00
  bond pdb=" C3  CAU A 501 "
       pdb=" C4  CAU A 501 "
    ideal  model  delta    sigma   weight residual
    1.412  1.372  0.040 2.00e-02 2.50e+03 3.93e+00
  bond pdb=" C8  CAU A 501 "
       pdb=" C9  CAU A 501 "
    ideal  model  delta    sigma   weight residual
    1.406  1.371  0.035 2.00e-02 2.50e+03 3.15e+00
  bond pdb=" CA  SER A 203 "
       pdb=" CB  SER A 203 "
    ideal  model  delta    sigma   weight residual
    1.528  1.504  0.025 1.56e-02 4.11e+03 2.49e+00
  ... (remaining 7300 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.30: 9777
        2.30 -     4.59: 111
        4.59 -     6.89: 19
        6.89 -     9.19: 2
        9.19 -    11.49: 3
  Bond angle restraints: 9912
  Sorted by residual:
  angle pdb=" C6  FK5 C 201 "
        pdb=" N7  FK5 C 201 "
        pdb=" C8  FK5 C 201 "
      ideal   model   delta    sigma   weight residual
     109.47  120.96  -11.49 3.00e+00 1.11e-01 1.47e+01
  angle pdb=" C2  FK5 C 201 "
        pdb=" N7  FK5 C 201 "
        pdb=" C6  FK5 C 201 "
      ideal   model   delta    sigma   weight residual
     109.47  120.48  -11.01 3.00e+00 1.11e-01 1.35e+01
  angle pdb=" N   GLN B 193 "
        pdb=" CA  GLN B 193 "
        pdb=" C   GLN B 193 "
      ideal   model   delta    sigma   weight residual
     114.56  110.40    4.16 1.27e+00 6.20e-01 1.07e+01
  angle pdb=" C2  FK5 C 201 "
        pdb=" N7  FK5 C 201 "
        pdb=" C8  FK5 C 201 "
      ideal   model   delta    sigma   weight residual
     109.47  118.55   -9.08 3.00e+00 1.11e-01 9.16e+00
  angle pdb=" CA  LEU B 364 "
        pdb=" CB  LEU B 364 "
        pdb=" CG  LEU B 364 "
      ideal   model   delta    sigma   weight residual
     116.30  106.32    9.98 3.50e+00 8.16e-02 8.14e+00
  ... (remaining 9907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.86: 4219
       33.86 -    67.71: 92
       67.71 -   101.57: 7
      101.57 -   135.43: 0
      135.43 -   169.28: 2
  Dihedral angle restraints: 4320
    sinusoidal: 1734
      harmonic: 2586
  Sorted by residual:
  dihedral pdb=" O14 CAU A 501 "
           pdb=" C15 CAU A 501 "
           pdb=" C16 CAU A 501 "
           pdb=" O17 CAU A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      54.74 -135.98 -169.28     1      3.00e+01 1.11e-03 2.11e+01
  dihedral pdb=" C18 CAU A 501 "
           pdb=" C15 CAU A 501 "
           pdb=" C16 CAU A 501 "
           pdb=" O14 CAU A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     179.20   16.56  162.64     1      3.00e+01 1.11e-03 2.08e+01
  dihedral pdb=" CA  GLU A  62 "
           pdb=" C   GLU A  62 "
           pdb=" N   ARG A  63 "
           pdb=" CA  ARG A  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.36   20.64     0      5.00e+00 4.00e-02 1.70e+01
  ... (remaining 4317 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 719
       0.038 -    0.075: 313
       0.075 -    0.113: 68
       0.113 -    0.151: 13
       0.151 -    0.189: 2
  Chirality restraints: 1115
  Sorted by residual:
  chirality pdb=" C16 CAU A 501 "
            pdb=" C15 CAU A 501 "
            pdb=" C18 CAU A 501 "
            pdb=" O17 CAU A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.31    2.49   -0.19 2.00e-01 2.50e+01 8.90e-01
  chirality pdb=" CB  ILE A 426 "
            pdb=" CA  ILE A 426 "
            pdb=" CG1 ILE A 426 "
            pdb=" CG2 ILE A 426 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 7.00e-01
  chirality pdb=" CA  PHE A 223 "
            pdb=" N   PHE A 223 "
            pdb=" C   PHE A 223 "
            pdb=" CB  PHE A 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.23e-01
  ... (remaining 1112 not shown)

  Planarity restraints: 1248
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C  77 "    0.030 5.00e-02 4.00e+02   4.59e-02 3.37e+00
        pdb=" N   PRO C  78 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO C  78 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C  78 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 193 "    0.007 2.00e-02 2.50e+03   1.39e-02 1.93e+00
        pdb=" C   PHE A 193 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   PHE A 193 "    0.009 2.00e-02 2.50e+03
        pdb=" N   PHE A 194 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 280 "    0.011 2.00e-02 2.50e+03   1.06e-02 1.67e+00
        pdb=" CG  HIS B 280 "   -0.023 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 280 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 280 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 280 "    0.002 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 280 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1245 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 145
        2.70 -     3.25: 7080
        3.25 -     3.80: 10807
        3.80 -     4.35: 13634
        4.35 -     4.90: 23055
  Nonbonded interactions: 54721
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 293 "
            pdb=" O   PHE B 298 "
     model   vdw
     2.146 3.040
  nonbonded pdb=" OG  SER A 323 "
            pdb=" O   THR B  13 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" OG1 THR C   6 "
            pdb=" OE1 GLN C  70 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OH  TYR C  82 "
            pdb=" O3  FK5 C 201 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OD1 ASP A 231 "
            pdb=" NZ  LYS A 236 "
     model   vdw
     2.313 3.120
  ... (remaining 54716 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     20.140
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6540
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      :  0.004   0.057   7305  Z= 0.237
  Angle     :  0.664  11.487   9912  Z= 0.349
  Chirality :  0.043   0.189   1115
  Planarity :  0.003   0.046   1248
  Dihedral  : 14.884 169.282   2646
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  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: -0.53 (0.29), residues: 879
  helix:  0.33 (0.25), residues: 444
  sheet: -0.36 (0.60), residues: 74
  loop : -1.13 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 109 
 HIS   0.011   0.001   HIS B 280 
 PHE   0.019   0.002   PHE A 223 
 TYR   0.012   0.001   TYR B 259 
 ARG   0.002   0.000   ARG A 272 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
REVERT: C  100 ASP cc_start: 0.7046 (t70) cc_final: 0.6704 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1534
  time to fit residues: 23.3061
Evaluate side-chains
  79 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 66 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 35 optimal weight:    0.0070
   chunk 68 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    1.4006

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

Flipped N/Q/H residues before XYZ refinement:
A 197 GLN
A 435 ASN
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 332 GLN
C  94 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.198287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.157414 restraints weight = 8230.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.160253 restraints weight = 7211.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.162311 restraints weight = 6045.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.4119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6826
moved from start:          0.1155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7305  Z= 0.275
  Angle     :  0.654  11.924   9912  Z= 0.333
  Chirality :  0.044   0.137   1115
  Planarity :  0.005   0.075   1248
  Dihedral  :  8.841 142.689   1005
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 11.27 %
    Favored  : 87.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.29), residues: 879
  helix:  0.39 (0.25), residues: 449
  sheet: -0.60 (0.61), residues: 64
  loop : -1.04 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 109 
 HIS   0.007   0.001   HIS B 280 
 PHE   0.019   0.002   PHE A 242 
 TYR   0.027   0.002   TYR B 174 
 ARG   0.003   0.000   ARG B 291 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 1.875 
Fit side-chains
   revert: symmetry clash
REVERT: C  100 ASP cc_start: 0.7381 (t70) cc_final: 0.6918 (t0)
  outliers start: 12
  outliers final: 9
  residues processed: 81
  average time/residue: 0.1712
  time to fit residues: 20.2062
Evaluate side-chains
  83 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  215 MET
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain A residue  369 CYS
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  226 MET
Chi-restraints excluded: chain B residue  284 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 69 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 43 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   chunk 3 optimal weight:    0.1980
   chunk 38 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  94 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.196972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.155129 restraints weight = 8345.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.157156 restraints weight = 6583.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.159401 restraints weight = 5820.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.4076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6809
moved from start:          0.1352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7305  Z= 0.237
  Angle     :  0.615  11.754   9912  Z= 0.311
  Chirality :  0.042   0.133   1115
  Planarity :  0.004   0.061   1248
  Dihedral  :  7.872 111.300   1005
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 15.60 %
    Favored  : 82.44 %
  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: -0.34 (0.29), residues: 879
  helix:  0.54 (0.25), residues: 441
  sheet: -1.18 (0.58), residues: 70
  loop : -0.88 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 109 
 HIS   0.005   0.001   HIS B 280 
 PHE   0.015   0.002   PHE A 242 
 TYR   0.017   0.001   TYR B 139 
 ARG   0.002   0.000   ARG B 278 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.688 
Fit side-chains
REVERT: A  179 GLN cc_start: 0.8740 (pm20) cc_final: 0.8539 (tp-100)
REVERT: B  322 LYS cc_start: 0.7880 (mttm) cc_final: 0.7577 (mttm)
REVERT: C  100 ASP cc_start: 0.7314 (t70) cc_final: 0.6754 (t0)
  outliers start: 15
  outliers final: 10
  residues processed: 88
  average time/residue: 0.1477
  time to fit residues: 19.1029
Evaluate side-chains
  88 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  215 MET
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain A residue  369 CYS
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  226 MET
Chi-restraints excluded: chain B residue  280 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 39 optimal weight:    9.9990
   chunk 74 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 79 optimal weight:    0.3980
   chunk 65 optimal weight:   10.0000
   chunk 60 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
A 392 HIS
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS
C  94 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.196611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.155063 restraints weight = 8398.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.157193 restraints weight = 6532.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.159409 restraints weight = 5735.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.4082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6801
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   7305  Z= 0.225
  Angle     :  0.637  11.843   9912  Z= 0.321
  Chirality :  0.043   0.220   1115
  Planarity :  0.004   0.053   1248
  Dihedral  :  7.429  89.222   1005
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 17.56 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.12 %
  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: -0.34 (0.29), residues: 879
  helix:  0.57 (0.26), residues: 441
  sheet: -1.27 (0.58), residues: 70
  loop : -0.90 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 109 
 HIS   0.005   0.001   HIS C  94 
 PHE   0.015   0.001   PHE A 242 
 TYR   0.016   0.001   TYR B 139 
 ARG   0.002   0.000   ARG B 278 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 78
  time to evaluate  : 0.772 
Fit side-chains
REVERT: B   73 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7275 (pm20)
REVERT: B  322 LYS cc_start: 0.7865 (mttm) cc_final: 0.7575 (mttm)
REVERT: C  100 ASP cc_start: 0.7318 (t70) cc_final: 0.6744 (t0)
  outliers start: 22
  outliers final: 12
  residues processed: 93
  average time/residue: 0.1577
  time to fit residues: 21.1575
Evaluate side-chains
  86 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  215 MET
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  369 CYS
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  226 MET
Chi-restraints excluded: chain B residue  280 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 73 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 59 optimal weight:    0.0270
   chunk 8 optimal weight:    0.9990
   chunk 3 optimal weight:    0.2980
   chunk 46 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 14 optimal weight:   10.0000
   overall best weight:    0.5640

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

Flipped N/Q/H residues before XYZ refinement:
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  94 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.199858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.159107 restraints weight = 8258.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.161908 restraints weight = 6411.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.163934 restraints weight = 5426.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.4123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6715
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7305  Z= 0.165
  Angle     :  0.587  11.312   9912  Z= 0.296
  Chirality :  0.041   0.166   1115
  Planarity :  0.004   0.048   1248
  Dihedral  :  6.827  68.048   1005
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 18.87 %
    Favored  : 78.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.24 (0.29), residues: 879
  helix:  0.66 (0.26), residues: 450
  sheet: -1.27 (0.58), residues: 70
  loop : -0.88 (0.34), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 109 
 HIS   0.005   0.001   HIS C  94 
 PHE   0.015   0.001   PHE A 242 
 TYR   0.014   0.001   TYR B 174 
 ARG   0.002   0.000   ARG B 278 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.755 
Fit side-chains
REVERT: A  145 LEU cc_start: 0.4125 (OUTLIER) cc_final: 0.3883 (tt)
REVERT: B   73 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7254 (pm20)
REVERT: B  174 TYR cc_start: 0.7193 (OUTLIER) cc_final: 0.6843 (t80)
REVERT: B  322 LYS cc_start: 0.7857 (mttm) cc_final: 0.7525 (mttm)
REVERT: C  100 ASP cc_start: 0.7322 (t70) cc_final: 0.6769 (t0)
  outliers start: 22
  outliers final: 15
  residues processed: 98
  average time/residue: 0.1503
  time to fit residues: 21.6477
Evaluate side-chains
  94 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  215 MET
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  367 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 15 optimal weight:   10.0000
   chunk 79 optimal weight:    7.9990
   chunk 83 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 87 optimal weight:    0.5980
   chunk 71 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 77 optimal weight:    0.6980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN
A 441 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.199232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.159846 restraints weight = 8531.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.160570 restraints weight = 8302.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.163531 restraints weight = 7315.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.4215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6994
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7305  Z= 0.206
  Angle     :  0.608  11.582   9912  Z= 0.304
  Chirality :  0.042   0.137   1115
  Planarity :  0.004   0.047   1248
  Dihedral  :  6.790  59.173   1005
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.00 %
    Favored  : 77.72 %
  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: -0.26 (0.29), residues: 879
  helix:  0.61 (0.25), residues: 451
  sheet: -0.97 (0.56), residues: 80
  loop : -0.92 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A  99 
 HIS   0.004   0.001   HIS B 280 
 PHE   0.014   0.001   PHE A 290 
 TYR   0.014   0.001   TYR B 139 
 ARG   0.002   0.000   ARG B 278 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 78
  time to evaluate  : 0.824 
Fit side-chains
REVERT: A  107 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6392 (mp0)
REVERT: A  145 LEU cc_start: 0.4597 (OUTLIER) cc_final: 0.4315 (tt)
REVERT: B   73 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7477 (pm20)
REVERT: B  223 TYR cc_start: 0.7005 (p90) cc_final: 0.6805 (p90)
REVERT: C   30 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7278 (mp)
REVERT: C  100 ASP cc_start: 0.7366 (t70) cc_final: 0.6843 (t0)
  outliers start: 25
  outliers final: 15
  residues processed: 97
  average time/residue: 0.1575
  time to fit residues: 22.4814
Evaluate side-chains
  94 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   99 TRP
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  215 MET
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain A residue  369 CYS
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain C residue   30 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 68 optimal weight:    5.9990
   chunk 59 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 5 optimal weight:    0.2980
   chunk 26 optimal weight:    0.6980
   chunk 58 optimal weight:    0.3980
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.6182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.202189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.166082 restraints weight = 8712.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.165327 restraints weight = 10146.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.166914 restraints weight = 8207.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.4232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7305  Z= 0.170
  Angle     :  0.599  11.332   9912  Z= 0.300
  Chirality :  0.041   0.226   1115
  Planarity :  0.004   0.047   1248
  Dihedral  :  6.680  63.374   1005
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.66 %
    Favored  : 77.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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: -0.17 (0.30), residues: 879
  helix:  0.67 (0.26), residues: 453
  sheet: -0.96 (0.56), residues: 80
  loop : -0.84 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A  99 
 HIS   0.004   0.001   HIS B 280 
 PHE   0.013   0.001   PHE A 242 
 TYR   0.014   0.001   TYR B 174 
 ARG   0.002   0.000   ARG B 278 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 82
  time to evaluate  : 0.803 
Fit side-chains
REVERT: A  145 LEU cc_start: 0.4706 (OUTLIER) cc_final: 0.4381 (tt)
REVERT: A  362 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6609 (mtp85)
REVERT: B   73 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7521 (pm20)
REVERT: B  223 TYR cc_start: 0.6957 (p90) cc_final: 0.6721 (p90)
REVERT: B  276 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7773 (mm)
REVERT: B  322 LYS cc_start: 0.8021 (mttm) cc_final: 0.7741 (mttm)
REVERT: C  100 ASP cc_start: 0.7337 (t70) cc_final: 0.6844 (t0)
  outliers start: 25
  outliers final: 17
  residues processed: 101
  average time/residue: 0.1694
  time to fit residues: 24.1572
Evaluate side-chains
  98 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   99 TRP
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  215 MET
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain A residue  362 ARG
Chi-restraints excluded: chain A residue  369 CYS
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  289 MET
Chi-restraints excluded: chain B residue  367 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 46 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    1.0784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.199737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.161414 restraints weight = 8761.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.161293 restraints weight = 10913.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.163591 restraints weight = 8747.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.4199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7048
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7305  Z= 0.222
  Angle     :  0.629  11.701   9912  Z= 0.314
  Chirality :  0.042   0.194   1115
  Planarity :  0.004   0.046   1248
  Dihedral  :  6.750  68.315   1005
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 20.05 %
    Favored  : 76.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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: -0.23 (0.29), residues: 879
  helix:  0.63 (0.26), residues: 445
  sheet: -1.03 (0.56), residues: 80
  loop : -0.85 (0.35), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A  99 
 HIS   0.005   0.001   HIS B 280 
 PHE   0.015   0.001   PHE A 290 
 TYR   0.014   0.001   TYR B 139 
 ARG   0.002   0.000   ARG B 278 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 76
  time to evaluate  : 0.813 
Fit side-chains
REVERT: A  145 LEU cc_start: 0.4680 (OUTLIER) cc_final: 0.4373 (tt)
REVERT: A  362 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.6630 (mtp85)
REVERT: B   73 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7532 (pm20)
REVERT: B  276 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7793 (mm)
REVERT: C  100 ASP cc_start: 0.7381 (t70) cc_final: 0.6873 (t0)
  outliers start: 28
  outliers final: 20
  residues processed: 98
  average time/residue: 0.1629
  time to fit residues: 22.9831
Evaluate side-chains
  98 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 74
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   99 TRP
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  184 CYS
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  215 MET
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  362 ARG
Chi-restraints excluded: chain A residue  369 CYS
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  444 PHE
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  289 MET
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain C residue   55 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 49 optimal weight:    0.2980
   chunk 31 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0050
   chunk 14 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
A 183 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.202317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.163749 restraints weight = 8733.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.164973 restraints weight = 9806.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.167481 restraints weight = 7648.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.4224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6980
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7305  Z= 0.166
  Angle     :  0.595  11.388   9912  Z= 0.296
  Chirality :  0.041   0.177   1115
  Planarity :  0.004   0.048   1248
  Dihedral  :  6.547  69.968   1005
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 21.10 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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: -0.08 (0.30), residues: 879
  helix:  0.77 (0.26), residues: 444
  sheet: -0.97 (0.56), residues: 80
  loop : -0.80 (0.35), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A  99 
 HIS   0.003   0.001   HIS A 178 
 PHE   0.012   0.001   PHE A 290 
 TYR   0.014   0.001   TYR B 174 
 ARG   0.002   0.000   ARG B 278 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 71
  time to evaluate  : 0.743 
Fit side-chains
REVERT: A  145 LEU cc_start: 0.4665 (OUTLIER) cc_final: 0.4343 (tt)
REVERT: A  362 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6596 (mtp85)
REVERT: B   73 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7460 (pm20)
REVERT: B  276 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7793 (mm)
REVERT: C  100 ASP cc_start: 0.7309 (t70) cc_final: 0.6810 (t0)
  outliers start: 22
  outliers final: 17
  residues processed: 88
  average time/residue: 0.1706
  time to fit residues: 21.5227
Evaluate side-chains
  92 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   99 TRP
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  215 MET
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain A residue  362 ARG
Chi-restraints excluded: chain A residue  369 CYS
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  444 PHE
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  289 MET
Chi-restraints excluded: chain B residue  367 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 76 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 49 optimal weight:    0.1980
   chunk 54 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.203431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.166724 restraints weight = 8848.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.168751 restraints weight = 9512.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.171157 restraints weight = 7728.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.4281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6939
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7305  Z= 0.174
  Angle     :  0.594  11.435   9912  Z= 0.293
  Chirality :  0.041   0.163   1115
  Planarity :  0.004   0.047   1248
  Dihedral  :  6.509  72.146   1005
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 21.10 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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: -0.07 (0.30), residues: 879
  helix:  0.79 (0.26), residues: 444
  sheet: -0.99 (0.56), residues: 80
  loop : -0.80 (0.35), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A  99 
 HIS   0.004   0.001   HIS B 280 
 PHE   0.014   0.001   PHE A 290 
 TYR   0.015   0.001   TYR B 139 
 ARG   0.002   0.000   ARG B 278 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 72
  time to evaluate  : 0.799 
Fit side-chains
REVERT: A  145 LEU cc_start: 0.4666 (OUTLIER) cc_final: 0.4354 (tt)
REVERT: A  362 ARG cc_start: 0.6821 (OUTLIER) cc_final: 0.6580 (mtp85)
REVERT: B   73 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7479 (pm20)
REVERT: B  276 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7802 (mm)
REVERT: C  100 ASP cc_start: 0.7353 (t70) cc_final: 0.6836 (t0)
  outliers start: 21
  outliers final: 17
  residues processed: 87
  average time/residue: 0.1698
  time to fit residues: 21.1451
Evaluate side-chains
  90 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 69
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   99 TRP
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  215 MET
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  316 MET
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain A residue  362 ARG
Chi-restraints excluded: chain A residue  369 CYS
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  289 MET
Chi-restraints excluded: chain B residue  367 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 50 optimal weight:    9.9990
   chunk 22 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0670
   chunk 71 optimal weight:    0.9990
   chunk 67 optimal weight:    5.9990
   chunk 51 optimal weight:    0.6980
   chunk 84 optimal weight:    5.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.6720

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.202431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.164955 restraints weight = 8765.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.165252 restraints weight = 10244.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.167675 restraints weight = 8400.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.4239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6980
moved from start:          0.2340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7305  Z= 0.169
  Angle     :  0.594  11.419   9912  Z= 0.294
  Chirality :  0.041   0.158   1115
  Planarity :  0.004   0.047   1248
  Dihedral  :  6.438  73.336   1005
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 20.58 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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: -0.03 (0.30), residues: 879
  helix:  0.82 (0.26), residues: 444
  sheet: -0.95 (0.56), residues: 80
  loop : -0.77 (0.35), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A  99 
 HIS   0.004   0.001   HIS B 280 
 PHE   0.013   0.001   PHE A 290 
 TYR   0.014   0.001   TYR B 139 
 ARG   0.002   0.000   ARG B 278 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2184.61 seconds
wall clock time: 40 minutes 7.68 seconds (2407.68 seconds total)