Starting phenix.real_space_refine
on Fri Feb 14 20:19:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7udc_26456/02_2025/7udc_26456.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7udc_26456/02_2025/7udc_26456.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7udc_26456/02_2025/7udc_26456.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7udc_26456/02_2025/7udc_26456.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7udc_26456/02_2025/7udc_26456.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7udc_26456/02_2025/7udc_26456.cif"
  }
  resolution = 3.7
  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
  Anisotropic ADP refinement not supported. Converting 5307 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      35      5.16       5
     C    4030      2.51       5
     N    1092      2.21       5
     O    1268      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 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: 6425
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 542, 4331
          Classifications: {'peptide': 542}
          Link IDs: {'PTRANS': 27, 'TRANS': 514}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 1716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1716
          Classifications: {'peptide': 215}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 2, 'TRANS': 212}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "C"
      Number of atoms: 378
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 378
          Classifications: {'peptide': 49}
          Link IDs: {'TRANS': 48}
  Time building chain proxies: 4.08, per 1000 atoms: 0.64
  Number of scatterers: 6425
  At special positions: 0
  Unit cell: (92.88, 109.08, 91.8, 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      35     16.00
     O    1268      8.00
     N    1092      7.00
     C    4030      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 205 " - pdb=" SG  CYS C  36 " 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: 1.53
  Conformation dependent library (CDL) restraints added in 874.8 milliseconds
  

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1560

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 3 sheets defined
      63.3% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 18
    Processing helix  chain 'A' and resid 34 through 45
      removed outlier: 3.631A  pdb=" N   CYS A  44 " --> pdb=" O   MET A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 52
    Processing helix  chain 'A' and resid 80 through 91
      removed outlier: 3.942A  pdb=" N   PHE A  91 " --> pdb=" O   LEU A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 121
    Processing helix  chain 'A' and resid 122 through 126
      removed outlier: 4.347A  pdb=" N   VAL A 126 " --> pdb=" O   ARG A 122 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 122 through 126'
    Processing helix  chain 'A' and resid 151 through 158
      removed outlier: 3.745A  pdb=" N   SER A 155 " --> pdb=" O   ASP A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 183
      removed outlier: 3.581A  pdb=" N   THR A 178 " --> pdb=" O   GLU A 174 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU A 179 " --> pdb=" O   GLN A 175 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   CYS A 180 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 216
    Processing helix  chain 'A' and resid 248 through 257
    Processing helix  chain 'A' and resid 285 through 292
      removed outlier: 3.816A  pdb=" N   ILE A 289 " --> pdb=" O   ASP A 285 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ALA A 290 " --> pdb=" O   ASP A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 313
      removed outlier: 4.065A  pdb=" N   SER A 300 " --> pdb=" O   ILE A 296 " (cutoff:3.500A)
      removed outlier: 4.935A  pdb=" N   GLN A 301 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 359
      Proline residue:  A 335  - end of helix
    Processing helix  chain 'A' and resid 361 through 375
      removed outlier: 3.893A  pdb=" N   ASP A 371 " --> pdb=" O   ARG A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 395
      Proline residue:  A 392  - end of helix
      removed outlier: 3.529A  pdb=" N   LEU A 395 " --> pdb=" O   VAL A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 415
      removed outlier: 3.741A  pdb=" N   TYR A 411 " --> pdb=" O   ILE A 407 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ILE A 412 " --> pdb=" O   ILE A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 431
    Processing helix  chain 'A' and resid 436 through 443
      removed outlier: 4.304A  pdb=" N   ILE A 440 " --> pdb=" O   ASP A 436 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   THR A 441 " --> pdb=" O   SER A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 447
    Processing helix  chain 'A' and resid 480 through 491
      removed outlier: 3.848A  pdb=" N   ASP A 484 " --> pdb=" O   PRO A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 561
      removed outlier: 3.958A  pdb=" N   ARG A 551 " --> pdb=" O   LEU A 547 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ALA A 553 " --> pdb=" O   GLU A 549 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   TYR A 554 " --> pdb=" O   MET A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 583
      removed outlier: 3.708A  pdb=" N   LEU A 579 " --> pdb=" O   PRO A 575 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LYS A 583 " --> pdb=" O   LEU A 579 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 12
    Processing helix  chain 'B' and resid 28 through 64
    Processing helix  chain 'B' and resid 68 through 102
    Processing helix  chain 'B' and resid 103 through 108
      removed outlier: 4.132A  pdb=" N   ASN B 107 " --> pdb=" O   GLU B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 149
    Processing helix  chain 'B' and resid 162 through 168
    Processing helix  chain 'B' and resid 179 through 193
    Processing helix  chain 'B' and resid 204 through 221
      removed outlier: 3.849A  pdb=" N   GLU B 211 " --> pdb=" O   ASN B 207 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   MET B 215 " --> pdb=" O   GLU B 211 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   PHE B 216 " --> pdb=" O   LEU B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 224
      No H-bonds generated for 'chain 'B' and resid 222 through 224'
    Processing helix  chain 'B' and resid 228 through 231
      removed outlier: 3.756A  pdb=" N   ASP B 231 " --> pdb=" O   GLU B 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 228 through 231'
    Processing helix  chain 'B' and resid 232 through 240
    Processing helix  chain 'C' and resid 34 through 36
      No H-bonds generated for 'chain 'C' and resid 34 through 36'
    Processing helix  chain 'C' and resid 37 through 73
      removed outlier: 4.112A  pdb=" N   GLU C  41 " --> pdb=" O   ALA C  37 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE C  45 " --> pdb=" O   GLU C  41 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 77
      removed outlier: 4.021A  pdb=" N   PHE C  77 " --> pdb=" O   ALA C  74 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 74 through 77'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 60
      removed outlier: 6.050A  pdb=" N   LYS A  29 " --> pdb=" O   ILE A  55 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   ILE A  57 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   VAL A  30 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
      removed outlier: 7.213A  pdb=" N   LEU A  76 " --> pdb=" O   VAL A  30 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   VAL A  32 " --> pdb=" O   LEU A  76 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   ALA A  73 " --> pdb=" O   HIS A 103 " (cutoff:3.500A)
      removed outlier: 7.397A  pdb=" N   PHE A 105 " --> pdb=" O   ALA A  73 " (cutoff:3.500A)
      removed outlier: 6.011A  pdb=" N   TYR A  75 " --> pdb=" O   PHE A 105 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   ALA A 102 " --> pdb=" O   ILE A 127 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   THR A 129 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139
      removed outlier: 6.659A  pdb=" N   TYR A 145 " --> pdb=" O   SER A 569 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   LEU A 537 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
      removed outlier: 7.683A  pdb=" N   GLY A 568 " --> pdb=" O   LEU A 537 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   ILE A 539 " --> pdb=" O   GLY A 568 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLN A 229 " --> pdb=" O   ARG A 536 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 266

    353 hydrogen bonds defined for protein.
    1050 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: 1.76

  Time building geometry restraints manager: 1.81 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: 2154
        1.34 -     1.46: 1282
        1.46 -     1.58: 3018
        1.58 -     1.70: 1
        1.70 -     1.82: 61
  Bond restraints: 6516
  Sorted by residual:
  bond pdb=" CB  PRO A 223 "
       pdb=" CG  PRO A 223 "
    ideal  model  delta    sigma   weight residual
    1.492  1.618 -0.126 5.00e-02 4.00e+02 6.32e+00
  bond pdb=" N   PRO A 433 "
       pdb=" CA  PRO A 433 "
    ideal  model  delta    sigma   weight residual
    1.457  1.469 -0.012 1.31e-02 5.83e+03 8.11e-01
  bond pdb=" CB  ASP C  65 "
       pdb=" CG  ASP C  65 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 2.50e-02 1.60e+03 7.54e-01
  bond pdb=" CA  THR B  23 "
       pdb=" CB  THR B  23 "
    ideal  model  delta    sigma   weight residual
    1.529  1.540 -0.011 1.62e-02 3.81e+03 4.97e-01
  bond pdb=" CA  THR B 161 "
       pdb=" CB  THR B 161 "
    ideal  model  delta    sigma   weight residual
    1.540  1.521  0.019 2.70e-02 1.37e+03 4.82e-01
  ... (remaining 6511 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 8626
        1.75 -     3.50: 122
        3.50 -     5.26: 25
        5.26 -     7.01: 2
        7.01 -     8.76: 1
  Bond angle restraints: 8776
  Sorted by residual:
  angle pdb=" CA  PRO A 223 "
        pdb=" N   PRO A 223 "
        pdb=" CD  PRO A 223 "
      ideal   model   delta    sigma   weight residual
     112.00  105.69    6.31 1.40e+00 5.10e-01 2.03e+01
  angle pdb=" CB  MET A 374 "
        pdb=" CG  MET A 374 "
        pdb=" SD  MET A 374 "
      ideal   model   delta    sigma   weight residual
     112.70  121.46   -8.76 3.00e+00 1.11e-01 8.53e+00
  angle pdb=" N   GLU B  73 "
        pdb=" CA  GLU B  73 "
        pdb=" CB  GLU B  73 "
      ideal   model   delta    sigma   weight residual
     110.28  114.20   -3.92 1.55e+00 4.16e-01 6.39e+00
  angle pdb=" C   ARG A 275 "
        pdb=" N   VAL A 276 "
        pdb=" CA  VAL A 276 "
      ideal   model   delta    sigma   weight residual
     121.97  126.52   -4.55 1.80e+00 3.09e-01 6.38e+00
  angle pdb=" N   PRO A 223 "
        pdb=" CD  PRO A 223 "
        pdb=" CG  PRO A 223 "
      ideal   model   delta    sigma   weight residual
     103.20   99.51    3.69 1.50e+00 4.44e-01 6.04e+00
  ... (remaining 8771 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 3646
       17.89 -    35.78: 349
       35.78 -    53.66: 67
       53.66 -    71.55: 18
       71.55 -    89.44: 5
  Dihedral angle restraints: 4085
    sinusoidal: 1702
      harmonic: 2383
  Sorted by residual:
  dihedral pdb=" CB  GLU A  66 "
           pdb=" CG  GLU A  66 "
           pdb=" CD  GLU A  66 "
           pdb=" OE1 GLU A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.44  -89.44     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CA  ASN B  50 "
           pdb=" CB  ASN B  50 "
           pdb=" CG  ASN B  50 "
           pdb=" OD1 ASN B  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -153.56   63.56     2      2.00e+01 2.50e-03 9.62e+00
  dihedral pdb=" CA  ASP B  27 "
           pdb=" CB  ASP B  27 "
           pdb=" CG  ASP B  27 "
           pdb=" OD1 ASP B  27 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -83.15   53.15     1      2.00e+01 2.50e-03 9.61e+00
  ... (remaining 4082 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 678
       0.032 -    0.064: 225
       0.064 -    0.096: 76
       0.096 -    0.127: 22
       0.127 -    0.159: 5
  Chirality restraints: 1006
  Sorted by residual:
  chirality pdb=" CA  PRO A 223 "
            pdb=" N   PRO A 223 "
            pdb=" C   PRO A 223 "
            pdb=" CB  PRO A 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.33e-01
  chirality pdb=" CA  ILE A 271 "
            pdb=" N   ILE A 271 "
            pdb=" C   ILE A 271 "
            pdb=" CB  ILE A 271 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.49e-01
  chirality pdb=" CA  GLU B  73 "
            pdb=" N   GLU B  73 "
            pdb=" C   GLU B  73 "
            pdb=" CB  GLU B  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.58e-01
  ... (remaining 1003 not shown)

  Planarity restraints: 1129
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 222 "   -0.065 5.00e-02 4.00e+02   9.56e-02 1.46e+01
        pdb=" N   PRO A 223 "    0.165 5.00e-02 4.00e+02
        pdb=" CA  PRO A 223 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 223 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 369 "    0.008 2.00e-02 2.50e+03   1.63e-02 2.65e+00
        pdb=" C   GLU A 369 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   GLU A 369 "    0.011 2.00e-02 2.50e+03
        pdb=" N   GLN A 370 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  78 "    0.027 5.00e-02 4.00e+02   4.00e-02 2.56e+00
        pdb=" N   PRO A  79 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A  79 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A  79 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1126 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 512
        2.74 -     3.28: 6563
        3.28 -     3.82: 10244
        3.82 -     4.36: 11465
        4.36 -     4.90: 20211
  Nonbonded interactions: 48995
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A  29 "
            pdb=" OE1 GLU A  72 "
     model   vdw
     2.200 3.120
  nonbonded pdb=" OH  TYR A  75 "
            pdb=" OD2 ASP A  90 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   GLN A 175 "
            pdb=" OG1 THR A 178 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" NH1 ARG A 464 "
            pdb=" OD2 ASP A 484 "
     model   vdw
     2.307 3.120
  nonbonded pdb=" OD1 ASN A 442 "
            pdb=" ND2 ASN A 586 "
     model   vdw
     2.316 3.120
  ... (remaining 48990 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:             0.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.360
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
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   0.126   6516  Z= 0.188
  Angle     :  0.539   8.760   8776  Z= 0.296
  Chirality :  0.038   0.159   1006
  Planarity :  0.004   0.096   1129
  Dihedral  : 14.902  89.440   2522
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  0.28 %
    Favored  : 99.44 %
  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:  1.79 (0.31), residues: 788
  helix:  2.44 (0.25), residues: 447
  sheet:  0.47 (0.78), residues: 54
  loop : -0.74 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 563 
 HIS   0.007   0.001   HIS B 213 
 PHE   0.017   0.001   PHE B  33 
 TYR   0.013   0.001   TYR A 531 
 ARG   0.003   0.000   ARG A 305 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 138
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.8709 (tpp) cc_final: 0.8468 (tpp)
REVERT: B   45 ASP cc_start: 0.8487 (t0) cc_final: 0.7605 (t0)
REVERT: B   98 GLN cc_start: 0.8250 (tm-30) cc_final: 0.8027 (tm-30)
REVERT: B  141 TYR cc_start: 0.9249 (t80) cc_final: 0.9010 (t80)
REVERT: C   62 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8241 (tm-30)
  outliers start: 2
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1544
  time to fit residues: 29.3201
Evaluate side-chains
  107 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 31 optimal weight:    8.9990
   chunk 61 optimal weight:    5.9990
   chunk 23 optimal weight:    0.0970
   chunk 37 optimal weight:    0.0970
   chunk 46 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 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 = 0.3784 r_free = 0.3784 target = 0.156062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.116466 restraints weight = 8210.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.114500 restraints weight = 5351.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.116570 restraints weight = 6039.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.1050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6516  Z= 0.185
  Angle     :  0.506   7.368   8776  Z= 0.269
  Chirality :  0.039   0.144   1006
  Planarity :  0.004   0.045   1129
  Dihedral  :  3.515  13.389    864
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  8.33 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.30), residues: 788
  helix:  2.53 (0.24), residues: 453
  sheet:  0.58 (0.75), residues: 55
  loop : -0.76 (0.35), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 288 
 HIS   0.004   0.001   HIS B 239 
 PHE   0.011   0.001   PHE B 127 
 TYR   0.019   0.001   TYR B 243 
 ARG   0.002   0.000   ARG A 406 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
REVERT: A  305 ARG cc_start: 0.8209 (ttp80) cc_final: 0.7860 (tmm-80)
REVERT: A  387 MET cc_start: 0.8719 (mmm) cc_final: 0.8371 (mmm)
REVERT: A  428 GLN cc_start: 0.8795 (tp40) cc_final: 0.8391 (tp-100)
REVERT: B   30 MET cc_start: 0.7108 (tpp) cc_final: 0.6774 (tpp)
REVERT: B   45 ASP cc_start: 0.8316 (t0) cc_final: 0.7437 (t0)
REVERT: B   77 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7935 (tm-30)
REVERT: B  141 TYR cc_start: 0.9207 (t80) cc_final: 0.8751 (t80)
REVERT: C   62 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8591 (tm-30)
  outliers start: 12
  outliers final: 7
  residues processed: 123
  average time/residue: 0.1647
  time to fit residues: 27.6840
Evaluate side-chains
  113 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  492 ASP
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   35 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:    0.2980
   chunk 52 optimal weight:    2.9990
   chunk 31 optimal weight:    9.9990
   chunk 64 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 55 optimal weight:    9.9990
   chunk 76 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9980
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
B  58 HIS
B 207 ASN
** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.154865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.115570 restraints weight = 8397.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.115133 restraints weight = 6664.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.117159 restraints weight = 6454.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.1407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6516  Z= 0.280
  Angle     :  0.528   8.166   8776  Z= 0.276
  Chirality :  0.040   0.144   1006
  Planarity :  0.004   0.040   1129
  Dihedral  :  3.595  15.183    864
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 11.11 %
    Favored  : 86.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.30), residues: 788
  helix:  2.53 (0.24), residues: 453
  sheet:  0.46 (0.74), residues: 54
  loop : -0.84 (0.34), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 288 
 HIS   0.005   0.001   HIS A 347 
 PHE   0.009   0.001   PHE B  34 
 TYR   0.021   0.001   TYR B 243 
 ARG   0.005   0.000   ARG B  28 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
REVERT: A  305 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7935 (tmm-80)
REVERT: A  387 MET cc_start: 0.8694 (mmm) cc_final: 0.8344 (mmm)
REVERT: A  428 GLN cc_start: 0.8907 (tp40) cc_final: 0.8579 (tp-100)
REVERT: A  579 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8344 (mm)
REVERT: B   28 ARG cc_start: 0.7321 (mmm160) cc_final: 0.7062 (mmm160)
REVERT: B   45 ASP cc_start: 0.8316 (t0) cc_final: 0.7440 (t0)
REVERT: B   77 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7889 (tm-30)
REVERT: B  141 TYR cc_start: 0.9218 (t80) cc_final: 0.8653 (t80)
REVERT: B  217 MET cc_start: 0.9085 (mmm) cc_final: 0.8752 (mmm)
REVERT: C   62 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8535 (tm-30)
REVERT: C   76 GLN cc_start: 0.8747 (tt0) cc_final: 0.8331 (mt0)
  outliers start: 15
  outliers final: 10
  residues processed: 122
  average time/residue: 0.1749
  time to fit residues: 29.0849
Evaluate side-chains
  122 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  492 ASP
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  207 ASN
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  224 GLU
Chi-restraints excluded: chain C residue   35 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 52 optimal weight:    0.5980
   chunk 60 optimal weight:    0.0030
   chunk 30 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 77 optimal weight:    3.9990
   chunk 68 optimal weight:    7.9990
   chunk 24 optimal weight:    0.1980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.4390

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

Flipped N/Q/H residues before XYZ refinement:
** B 236 ASN ** 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 = 0.3842 r_free = 0.3842 target = 0.162228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.120091 restraints weight = 8423.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.119413 restraints weight = 5322.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.121173 restraints weight = 5267.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6516  Z= 0.147
  Angle     :  0.492  11.838   8776  Z= 0.256
  Chirality :  0.038   0.143   1006
  Planarity :  0.003   0.039   1129
  Dihedral  :  3.515  13.678    864
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 12.36 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.30), residues: 788
  helix:  2.65 (0.24), residues: 453
  sheet:  0.44 (0.75), residues: 54
  loop : -0.77 (0.35), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 563 
 HIS   0.003   0.001   HIS B 239 
 PHE   0.013   0.001   PHE B 127 
 TYR   0.024   0.001   TYR B 243 
 ARG   0.004   0.000   ARG B  28 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 MET cc_start: 0.8789 (mmm) cc_final: 0.8544 (mmm)
REVERT: A  276 VAL cc_start: 0.9274 (m) cc_final: 0.8798 (p)
REVERT: A  305 ARG cc_start: 0.8254 (ttp80) cc_final: 0.7928 (tmm-80)
REVERT: A  355 MET cc_start: 0.9038 (tpp) cc_final: 0.8712 (mmm)
REVERT: A  374 MET cc_start: 0.8934 (mmm) cc_final: 0.8733 (mmm)
REVERT: A  387 MET cc_start: 0.8733 (mmm) cc_final: 0.8385 (mmm)
REVERT: B   30 MET cc_start: 0.7276 (tpp) cc_final: 0.7019 (tpp)
REVERT: B   45 ASP cc_start: 0.8253 (t0) cc_final: 0.7355 (t0)
REVERT: B   77 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7874 (tm-30)
REVERT: B  131 MET cc_start: 0.8891 (tpp) cc_final: 0.8473 (tpp)
REVERT: C   62 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8467 (tm-30)
REVERT: C   76 GLN cc_start: 0.8702 (tt0) cc_final: 0.8384 (mt0)
  outliers start: 11
  outliers final: 6
  residues processed: 120
  average time/residue: 0.1813
  time to fit residues: 29.1891
Evaluate side-chains
  110 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain C residue   35 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 69 optimal weight:   20.0000
   chunk 73 optimal weight:    4.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
** B 236 ASN ** 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 = 0.3751 r_free = 0.3751 target = 0.152875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.113073 restraints weight = 8429.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.111447 restraints weight = 5671.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.113510 restraints weight = 5661.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   6516  Z= 0.346
  Angle     :  0.577   9.496   8776  Z= 0.300
  Chirality :  0.041   0.144   1006
  Planarity :  0.004   0.038   1129
  Dihedral  :  3.676  17.308    864
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 12.92 %
    Favored  : 85.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.30), residues: 788
  helix:  2.54 (0.24), residues: 454
  sheet:  0.14 (0.71), residues: 55
  loop : -0.83 (0.35), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 288 
 HIS   0.005   0.001   HIS A 347 
 PHE   0.010   0.001   PHE B  34 
 TYR   0.024   0.002   TYR B 243 
 ARG   0.009   0.001   ARG B  28 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 MET cc_start: 0.8825 (mmm) cc_final: 0.8576 (mmm)
REVERT: A   47 MET cc_start: 0.9032 (tpp) cc_final: 0.8646 (tpp)
REVERT: A  238 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8292 (t0)
REVERT: A  387 MET cc_start: 0.8743 (mmm) cc_final: 0.8372 (mmm)
REVERT: B   30 MET cc_start: 0.7274 (tpp) cc_final: 0.7034 (tpp)
REVERT: B   45 ASP cc_start: 0.8253 (t0) cc_final: 0.7388 (t0)
REVERT: B   77 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7943 (tm-30)
REVERT: B   98 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7941 (tm-30)
REVERT: B  131 MET cc_start: 0.8856 (tpp) cc_final: 0.8532 (mpp)
REVERT: B  141 TYR cc_start: 0.9309 (t80) cc_final: 0.9000 (t80)
REVERT: C   62 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8490 (tm-30)
REVERT: C   65 ASP cc_start: 0.8585 (t0) cc_final: 0.8362 (t0)
REVERT: C   76 GLN cc_start: 0.8730 (tt0) cc_final: 0.8359 (mt0)
  outliers start: 13
  outliers final: 8
  residues processed: 114
  average time/residue: 0.1610
  time to fit residues: 25.6612
Evaluate side-chains
  111 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   50 ILE
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  238 ASP
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  492 ASP
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   35 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 76 optimal weight:    5.9990
   chunk 64 optimal weight:    9.9990
   chunk 77 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** B 236 ASN ** 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 = 0.3779 r_free = 0.3779 target = 0.155355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.115390 restraints weight = 8316.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.114231 restraints weight = 5474.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.116102 restraints weight = 5378.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6516  Z= 0.194
  Angle     :  0.521   9.597   8776  Z= 0.274
  Chirality :  0.039   0.143   1006
  Planarity :  0.004   0.040   1129
  Dihedral  :  3.584  15.296    864
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 14.58 %
    Favored  : 83.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.30), residues: 788
  helix:  2.63 (0.24), residues: 454
  sheet:  0.19 (0.72), residues: 55
  loop : -0.83 (0.35), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 288 
 HIS   0.003   0.001   HIS B 239 
 PHE   0.007   0.001   PHE B  33 
 TYR   0.026   0.001   TYR B 243 
 ARG   0.005   0.000   ARG B  28 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.753 
Fit side-chains
REVERT: A   15 MET cc_start: 0.8820 (mmm) cc_final: 0.8573 (mmm)
REVERT: A  238 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8304 (t0)
REVERT: A  276 VAL cc_start: 0.9279 (m) cc_final: 0.8807 (p)
REVERT: A  387 MET cc_start: 0.8691 (mmm) cc_final: 0.8296 (mmm)
REVERT: B   30 MET cc_start: 0.7083 (tpp) cc_final: 0.6848 (tpp)
REVERT: B   45 ASP cc_start: 0.8358 (t0) cc_final: 0.7424 (t0)
REVERT: B   77 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7813 (tm-30)
REVERT: B  131 MET cc_start: 0.8896 (tpp) cc_final: 0.8383 (mpp)
REVERT: B  217 MET cc_start: 0.8970 (mmm) cc_final: 0.8630 (mmm)
REVERT: C   62 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8486 (tm-30)
REVERT: C   76 GLN cc_start: 0.8729 (tt0) cc_final: 0.8411 (mt0)
  outliers start: 11
  outliers final: 8
  residues processed: 113
  average time/residue: 0.1569
  time to fit residues: 24.8082
Evaluate side-chains
  111 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  238 ASP
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  492 ASP
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   81 ASP
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   35 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 59 optimal weight:   10.0000
   chunk 77 optimal weight:    1.9990
   chunk 62 optimal weight:    7.9990
   chunk 74 optimal weight:    0.9990
   chunk 76 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
** B 236 ASN ** 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 = 0.3755 r_free = 0.3755 target = 0.153254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.113259 restraints weight = 8370.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.111677 restraints weight = 5632.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.113790 restraints weight = 5565.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6516  Z= 0.275
  Angle     :  0.552   8.502   8776  Z= 0.288
  Chirality :  0.040   0.144   1006
  Planarity :  0.004   0.040   1129
  Dihedral  :  3.660  17.194    864
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 15.00 %
    Favored  : 83.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.30), residues: 788
  helix:  2.55 (0.24), residues: 454
  sheet:  0.05 (0.71), residues: 55
  loop : -0.89 (0.34), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 288 
 HIS   0.009   0.001   HIS B  58 
 PHE   0.010   0.001   PHE B  34 
 TYR   0.027   0.002   TYR B 243 
 ARG   0.005   0.000   ARG B  28 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.768 
Fit side-chains
REVERT: A   15 MET cc_start: 0.8815 (mmm) cc_final: 0.8409 (mmm)
REVERT: A   47 MET cc_start: 0.9035 (tpp) cc_final: 0.8824 (tpt)
REVERT: A  238 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8374 (t0)
REVERT: A  275 ARG cc_start: 0.8560 (tpp-160) cc_final: 0.8241 (tpp-160)
REVERT: A  387 MET cc_start: 0.8697 (mmm) cc_final: 0.8299 (mmm)
REVERT: A  550 MET cc_start: 0.8854 (ttm) cc_final: 0.8481 (mtp)
REVERT: B    6 GLN cc_start: 0.8842 (tp40) cc_final: 0.8523 (tp40)
REVERT: B   30 MET cc_start: 0.7167 (tpp) cc_final: 0.6907 (tpp)
REVERT: B   45 ASP cc_start: 0.8373 (t0) cc_final: 0.7450 (t0)
REVERT: B   77 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7863 (tm-30)
REVERT: B  131 MET cc_start: 0.8850 (tpp) cc_final: 0.8317 (mpp)
REVERT: C   62 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8496 (tm-30)
REVERT: C   76 GLN cc_start: 0.8719 (tt0) cc_final: 0.8395 (mt0)
  outliers start: 14
  outliers final: 10
  residues processed: 116
  average time/residue: 0.1618
  time to fit residues: 26.0542
Evaluate side-chains
  117 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  238 ASP
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  492 ASP
Chi-restraints excluded: chain B residue   81 ASP
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   35 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 60 optimal weight:    0.0060
   chunk 22 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.8798

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

Flipped N/Q/H residues before XYZ refinement:
A 429 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.157962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.118020 restraints weight = 8292.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.117136 restraints weight = 5259.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.118934 restraints weight = 5225.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6516  Z= 0.196
  Angle     :  0.520   8.397   8776  Z= 0.273
  Chirality :  0.039   0.143   1006
  Planarity :  0.003   0.041   1129
  Dihedral  :  3.610  15.891    864
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 15.83 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.30), residues: 788
  helix:  2.57 (0.24), residues: 455
  sheet:  0.14 (0.71), residues: 55
  loop : -0.86 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 288 
 HIS   0.005   0.001   HIS B  58 
 PHE   0.007   0.001   PHE B  34 
 TYR   0.026   0.001   TYR B 243 
 ARG   0.004   0.000   ARG B  28 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.697 
Fit side-chains
REVERT: A   15 MET cc_start: 0.8804 (mmm) cc_final: 0.8393 (mmm)
REVERT: A  238 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8362 (t0)
REVERT: A  275 ARG cc_start: 0.8535 (tpp-160) cc_final: 0.8205 (tpp-160)
REVERT: A  276 VAL cc_start: 0.9270 (m) cc_final: 0.8804 (p)
REVERT: A  550 MET cc_start: 0.8808 (ttm) cc_final: 0.8437 (mtp)
REVERT: B    6 GLN cc_start: 0.8824 (tp40) cc_final: 0.8510 (tp40)
REVERT: B   30 MET cc_start: 0.7137 (tpp) cc_final: 0.6878 (tpp)
REVERT: B   45 ASP cc_start: 0.8371 (t0) cc_final: 0.7433 (t0)
REVERT: B   77 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7819 (tm-30)
REVERT: B  131 MET cc_start: 0.8784 (tpp) cc_final: 0.8264 (mpp)
REVERT: B  148 ARG cc_start: 0.7967 (ttm-80) cc_final: 0.7688 (ptp-110)
REVERT: B  217 MET cc_start: 0.8966 (mmm) cc_final: 0.8636 (mmm)
REVERT: C   62 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8479 (tm-30)
REVERT: C   76 GLN cc_start: 0.8730 (tt0) cc_final: 0.8444 (mt0)
  outliers start: 12
  outliers final: 11
  residues processed: 117
  average time/residue: 0.1538
  time to fit residues: 25.2766
Evaluate side-chains
  118 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  238 ASP
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  354 CYS
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  492 ASP
Chi-restraints excluded: chain B residue   81 ASP
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   35 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 37 optimal weight:    0.2980
   chunk 24 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 54 optimal weight:    5.9990
   chunk 34 optimal weight:    0.4980
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.3743 r_free = 0.3743 target = 0.152398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.112573 restraints weight = 8445.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.110604 restraints weight = 5498.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.112906 restraints weight = 5394.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6516  Z= 0.205
  Angle     :  0.540  10.781   8776  Z= 0.286
  Chirality :  0.039   0.142   1006
  Planarity :  0.004   0.041   1129
  Dihedral  :  3.577  16.180    864
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 15.42 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.30), residues: 788
  helix:  2.57 (0.24), residues: 455
  sheet:  0.10 (0.71), residues: 55
  loop : -0.82 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 563 
 HIS   0.005   0.001   HIS B  58 
 PHE   0.008   0.001   PHE B  34 
 TYR   0.027   0.001   TYR B 243 
 ARG   0.004   0.000   ARG A 122 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.730 
Fit side-chains
REVERT: A   15 MET cc_start: 0.8848 (mmm) cc_final: 0.8476 (mmm)
REVERT: A   47 MET cc_start: 0.9131 (tpp) cc_final: 0.8843 (tpp)
REVERT: A  238 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8300 (t0)
REVERT: A  275 ARG cc_start: 0.8474 (tpp-160) cc_final: 0.8191 (tpp-160)
REVERT: A  276 VAL cc_start: 0.9276 (m) cc_final: 0.8795 (p)
REVERT: A  550 MET cc_start: 0.8806 (ttm) cc_final: 0.8488 (mtp)
REVERT: A  579 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8452 (mm)
REVERT: B    6 GLN cc_start: 0.8802 (tp40) cc_final: 0.8522 (tp40)
REVERT: B   30 MET cc_start: 0.7199 (tpp) cc_final: 0.6934 (tpp)
REVERT: B   45 ASP cc_start: 0.8289 (t0) cc_final: 0.7365 (t0)
REVERT: B   77 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7822 (tm-30)
REVERT: B  148 ARG cc_start: 0.7905 (ttm-80) cc_final: 0.7628 (ptp-110)
REVERT: B  217 MET cc_start: 0.8995 (mmm) cc_final: 0.8633 (mmm)
REVERT: C   62 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8473 (tm-30)
REVERT: C   65 ASP cc_start: 0.8576 (t0) cc_final: 0.8346 (t0)
  outliers start: 15
  outliers final: 13
  residues processed: 116
  average time/residue: 0.1569
  time to fit residues: 25.6088
Evaluate side-chains
  119 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   50 ILE
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  238 ASP
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  354 CYS
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  492 ASP
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain B residue   81 ASP
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   35 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   chunk 75 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 68 optimal weight:    6.9990
   chunk 3 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 359 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.158625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.117828 restraints weight = 8372.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.118629 restraints weight = 5497.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.120227 restraints weight = 5250.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6516  Z= 0.185
  Angle     :  0.528  10.299   8776  Z= 0.277
  Chirality :  0.039   0.142   1006
  Planarity :  0.004   0.041   1129
  Dihedral  :  3.554  18.094    864
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 15.83 %
    Favored  : 82.08 %
  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:  1.89 (0.30), residues: 788
  helix:  2.59 (0.24), residues: 455
  sheet:  0.16 (0.72), residues: 55
  loop : -0.85 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 563 
 HIS   0.005   0.001   HIS B  58 
 PHE   0.013   0.001   PHE B 127 
 TYR   0.027   0.001   TYR B 243 
 ARG   0.005   0.000   ARG A 122 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 1.236 
Fit side-chains
REVERT: A   15 MET cc_start: 0.8813 (mmm) cc_final: 0.8418 (mmm)
REVERT: A   47 MET cc_start: 0.9055 (tpp) cc_final: 0.8771 (tpp)
REVERT: A  238 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8363 (t0)
REVERT: A  275 ARG cc_start: 0.8456 (tpp-160) cc_final: 0.8166 (tpp-160)
REVERT: A  276 VAL cc_start: 0.9251 (m) cc_final: 0.8799 (p)
REVERT: A  429 HIS cc_start: 0.8585 (t-170) cc_final: 0.8342 (t70)
REVERT: A  550 MET cc_start: 0.8765 (ttm) cc_final: 0.8403 (mtp)
REVERT: A  579 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8414 (mm)
REVERT: B    6 GLN cc_start: 0.8828 (tp40) cc_final: 0.8539 (tp40)
REVERT: B   30 MET cc_start: 0.7168 (tpp) cc_final: 0.6906 (tpp)
REVERT: B   45 ASP cc_start: 0.8340 (t0) cc_final: 0.7418 (t0)
REVERT: B   77 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7802 (tm-30)
REVERT: B  148 ARG cc_start: 0.7871 (ttm-80) cc_final: 0.7617 (ptp-110)
REVERT: B  217 MET cc_start: 0.8991 (mmm) cc_final: 0.8638 (mmm)
REVERT: C   62 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8483 (tm-30)
REVERT: C   65 ASP cc_start: 0.8647 (t0) cc_final: 0.8401 (t0)
  outliers start: 15
  outliers final: 12
  residues processed: 118
  average time/residue: 0.1649
  time to fit residues: 27.5079
Evaluate side-chains
  120 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  238 ASP
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  354 CYS
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  492 ASP
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain B residue   81 ASP
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   76 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 41 optimal weight:    0.0570
   chunk 33 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 64 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 67 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 65 optimal weight:    0.7980
   chunk 28 optimal weight:    0.3980
   overall best weight:    0.8300

-------------------------------------------------------------------------------
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 = 0.3811 r_free = 0.3811 target = 0.158909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.118306 restraints weight = 8518.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.117537 restraints weight = 5301.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.119273 restraints weight = 5229.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.2157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6516  Z= 0.194
  Angle     :  0.539  10.112   8776  Z= 0.286
  Chirality :  0.039   0.161   1006
  Planarity :  0.003   0.046   1129
  Dihedral  :  3.580  20.125    864
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 15.83 %
    Favored  : 81.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.30), residues: 788
  helix:  2.59 (0.24), residues: 455
  sheet:  0.20 (0.72), residues: 55
  loop : -0.82 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 563 
 HIS   0.005   0.001   HIS B  58 
 PHE   0.015   0.001   PHE B 127 
 TYR   0.027   0.001   TYR B 243 
 ARG   0.003   0.000   ARG B  28 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1904.09 seconds
wall clock time: 34 minutes 58.58 seconds (2098.58 seconds total)