Starting phenix.real_space_refine
on Tue Feb 11 17:54:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vrl_21370/02_2025/6vrl_21370.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vrl_21370/02_2025/6vrl_21370.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vrl_21370/02_2025/6vrl_21370.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vrl_21370/02_2025/6vrl_21370.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vrl_21370/02_2025/6vrl_21370.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vrl_21370/02_2025/6vrl_21370.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.971
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 92 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: 5
    Type Number    sf(0)   Gaussians
     I       1     10.91       5
     S      34      5.16       5
     C    4045      2.51       5
     N     958      2.21       5
     O    1103      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 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: 6141
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4311
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 541, 4311
          Classifications: {'peptide': 541}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 23, 'TRANS': 517}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "C"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 100}
    Chain: "B"
      Number of atoms: 924
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 924
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 5, 'TRANS': 111}
    Chain: "A"
      Number of atoms: 87
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 87
          Unusual residues: {'LMT': 1, 'NAG': 2, 'RFY': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 4.87, per 1000 atoms: 0.79
  Number of scatterers: 6141
  At special positions: 0
  Unit cell: (95.256, 104.328, 82.296, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     I       1     52.95
     S      34     16.00
     O    1103      8.00
     N     958      7.00
     C    4045      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  43 " - pdb=" SG  CYS C 108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  41 " - pdb=" SG  CYS B 115 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 701 " - " ASN A 208 "
      " NAG A 702 " - " ASN A 217 "
  Time building additional restraints: 1.64
  Conformation dependent library (CDL) restraints added in 821.4 milliseconds
  

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1406

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 7 sheets defined
      53.8% alpha, 8.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 84 through 97
      removed outlier: 3.540A  pdb=" N   PHE A  88 " --> pdb=" O   LYS A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 102
    Processing helix  chain 'A' and resid 104 through 112
    Processing helix  chain 'A' and resid 113 through 116
    Processing helix  chain 'A' and resid 117 through 128
    Processing helix  chain 'A' and resid 128 through 144
      removed outlier: 4.110A  pdb=" N   LEU A 132 " --> pdb=" O   GLY A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 158
    Processing helix  chain 'A' and resid 159 through 190
      removed outlier: 4.256A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   ASN A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   THR A 178 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   ILE A 179 " --> pdb=" O   TYR A 175 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   MET A 180 " --> pdb=" O   TYR A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 235
    Processing helix  chain 'A' and resid 253 through 271
    Processing helix  chain 'A' and resid 273 through 285
      removed outlier: 3.721A  pdb=" N   LYS A 279 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   VAL A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 300
      removed outlier: 3.665A  pdb=" N   ILE A 290 " --> pdb=" O   THR A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 314
      removed outlier: 4.080A  pdb=" N   VAL A 309 " --> pdb=" O   ALA A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 321
    Processing helix  chain 'A' and resid 322 through 338
      removed outlier: 4.094A  pdb=" N   TRP A 326 " --> pdb=" O   GLU A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 349
    Processing helix  chain 'A' and resid 356 through 390
      removed outlier: 3.531A  pdb=" N   ASP A 360 " --> pdb=" O   ASN A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 397
    Processing helix  chain 'A' and resid 403 through 408
    Processing helix  chain 'A' and resid 408 through 417
    Processing helix  chain 'A' and resid 419 through 454
      removed outlier: 4.039A  pdb=" N   PHE A 423 " --> pdb=" O   ALA A 419 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ASP A 437 " --> pdb=" O   THR A 433 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   SER A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 478
    Processing helix  chain 'A' and resid 479 through 481
      No H-bonds generated for 'chain 'A' and resid 479 through 481'
    Processing helix  chain 'A' and resid 484 through 496
      removed outlier: 3.832A  pdb=" N   VAL A 488 " --> pdb=" O   GLY A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 514
    Processing helix  chain 'A' and resid 517 through 530
    Processing helix  chain 'A' and resid 534 through 543
    Processing helix  chain 'A' and resid 543 through 557
    Processing helix  chain 'A' and resid 571 through 587
      removed outlier: 4.254A  pdb=" N   SER A 585 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   PHE A 586 " --> pdb=" O   GLY A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 596
    Processing helix  chain 'A' and resid 603 through 611
    Processing helix  chain 'B' and resid 81 through 84
      removed outlier: 4.011A  pdb=" N   LYS B  84 " --> pdb=" O   GLN B  81 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 81 through 84'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 565
      removed outlier: 3.666A  pdb=" N   LEU A 565 " --> pdb=" O   TYR A 568 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 24 through 26
    Processing sheet with id=AA3, first strand: chain 'C' and resid 39 through 41
    Processing sheet with id=AA4, first strand: chain 'C' and resid 73 through 74
      removed outlier: 6.797A  pdb=" N   TRP C  55 " --> pdb=" O   LEU C  67 " (cutoff:3.500A)
      removed outlier: 4.952A  pdb=" N   TYR C  69 " --> pdb=" O   VAL C  53 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   VAL C  53 " --> pdb=" O   TYR C  69 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 22 through 25
    Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 39
      removed outlier: 3.811A  pdb=" N   VAL B  37 " --> pdb=" O   LEU B 102 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LEU B 102 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ILE B  39 " --> pdb=" O   MET B 100 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   MET B 100 " --> pdb=" O   ILE B  39 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79
      removed outlier: 6.649A  pdb=" N   TRP B  55 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 5.538A  pdb=" N   ASN B  69 " --> pdb=" O   MET B  53 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   MET B  53 " --> pdb=" O   ASN B  69 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   VAL B 112 " --> pdb=" O   GLN B  58 " (cutoff:3.500A)

    312 hydrogen bonds defined for protein.
    888 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.73

  Time building geometry restraints manager: 1.86 seconds

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

  Histogram of bond lengths:
        1.23 -     1.40: 2681
        1.40 -     1.58: 3595
        1.58 -     1.75: 0
        1.75 -     1.93: 49
        1.93 -     2.11: 1
  Bond restraints: 6326
  Sorted by residual:
  bond pdb=" C06 RFY A 704 "
       pdb=" C07 RFY A 704 "
    ideal  model  delta    sigma   weight residual
    1.511  1.576 -0.065 2.00e-02 2.50e+03 1.06e+01
  bond pdb=" C05 RFY A 704 "
       pdb=" C06 RFY A 704 "
    ideal  model  delta    sigma   weight residual
    1.543  1.493  0.050 2.00e-02 2.50e+03 6.30e+00
  bond pdb=" C17 RFY A 704 "
       pdb=" C18 RFY A 704 "
    ideal  model  delta    sigma   weight residual
    1.370  1.418 -0.048 2.00e-02 2.50e+03 5.81e+00
  bond pdb=" C19 RFY A 704 "
       pdb=" C20 RFY A 704 "
    ideal  model  delta    sigma   weight residual
    1.371  1.416 -0.045 2.00e-02 2.50e+03 5.11e+00
  bond pdb=" C01 RFY A 704 "
       pdb=" C06 RFY A 704 "
    ideal  model  delta    sigma   weight residual
    1.542  1.498  0.044 2.00e-02 2.50e+03 4.95e+00
  ... (remaining 6321 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 8430
        1.79 -     3.57: 150
        3.57 -     5.36: 25
        5.36 -     7.15: 10
        7.15 -     8.94: 4
  Bond angle restraints: 8619
  Sorted by residual:
  angle pdb=" N   VAL A 397 "
        pdb=" CA  VAL A 397 "
        pdb=" C   VAL A 397 "
      ideal   model   delta    sigma   weight residual
     113.42  109.33    4.09 1.17e+00 7.31e-01 1.22e+01
  angle pdb=" N   ARG B 121 "
        pdb=" CA  ARG B 121 "
        pdb=" C   ARG B 121 "
      ideal   model   delta    sigma   weight residual
     109.81  117.12   -7.31 2.21e+00 2.05e-01 1.09e+01
  angle pdb=" C2  LMT A 703 "
        pdb=" C3  LMT A 703 "
        pdb=" C4  LMT A 703 "
      ideal   model   delta    sigma   weight residual
     117.09  108.15    8.94 3.00e+00 1.11e-01 8.87e+00
  angle pdb=" C10 LMT A 703 "
        pdb=" C9  LMT A 703 "
        pdb=" C8  LMT A 703 "
      ideal   model   delta    sigma   weight residual
     116.03  107.32    8.71 3.00e+00 1.11e-01 8.43e+00
  angle pdb=" C   VAL B 120 "
        pdb=" N   ARG B 121 "
        pdb=" CA  ARG B 121 "
      ideal   model   delta    sigma   weight residual
     121.80  128.79   -6.99 2.44e+00 1.68e-01 8.20e+00
  ... (remaining 8614 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 3299
       17.53 -    35.07: 321
       35.07 -    52.60: 54
       52.60 -    70.14: 14
       70.14 -    87.67: 4
  Dihedral angle restraints: 3692
    sinusoidal: 1478
      harmonic: 2214
  Sorted by residual:
  dihedral pdb=" CA  ARG B 121 "
           pdb=" C   ARG B 121 "
           pdb=" N   PRO B 122 "
           pdb=" CA  PRO B 122 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  128.14   51.86     0      5.00e+00 4.00e-02 1.08e+02
  dihedral pdb=" CB  CYS A 200 "
           pdb=" SG  CYS A 200 "
           pdb=" SG  CYS A 209 "
           pdb=" CB  CYS A 209 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  133.61  -40.61     1      1.00e+01 1.00e-02 2.31e+01
  dihedral pdb=" CA  CYS A 209 "
           pdb=" C   CYS A 209 "
           pdb=" N   THR A 210 "
           pdb=" CA  THR A 210 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.28   18.72     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 3689 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 714
       0.042 -    0.083: 207
       0.083 -    0.125: 40
       0.125 -    0.166: 1
       0.166 -    0.208: 4
  Chirality restraints: 966
  Sorted by residual:
  chirality pdb=" C4' LMT A 703 "
            pdb=" C3' LMT A 703 "
            pdb=" C5' LMT A 703 "
            pdb=" O1B LMT A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.76    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" C3B LMT A 703 "
            pdb=" C2B LMT A 703 "
            pdb=" C4B LMT A 703 "
            pdb=" O3B LMT A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50    2.29    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" C5' LMT A 703 "
            pdb=" C4' LMT A 703 "
            pdb=" C6' LMT A 703 "
            pdb=" O5' LMT A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.30   -0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 963 not shown)

  Planarity restraints: 1050
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 121 "   -0.044 5.00e-02 4.00e+02   6.70e-02 7.18e+00
        pdb=" N   PRO B 122 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO B 122 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 122 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 465 "   -0.010 2.00e-02 2.50e+03   1.97e-02 3.90e+00
        pdb=" C   PHE A 465 "    0.034 2.00e-02 2.50e+03
        pdb=" O   PHE A 465 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   VAL A 466 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 589 "    0.020 5.00e-02 4.00e+02   3.03e-02 1.47e+00
        pdb=" N   PRO A 590 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 590 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 590 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1047 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.72: 256
        2.72 -     3.28: 6880
        3.28 -     3.84: 11030
        3.84 -     4.40: 13024
        4.40 -     4.96: 22133
  Nonbonded interactions: 53323
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C  83 "
            pdb=" O   THR C  94 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" OG  SER B 110 "
            pdb=" O   LEU B 134 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" O   THR A 221 "
            pdb=" OG  SER A 224 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   ASP C 102 "
            pdb=" OH  TYR C 106 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   SER A 559 "
            pdb=" O6' LMT A 703 "
     model   vdw
     2.267 3.040
  ... (remaining 53318 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.580
  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:2.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6910
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   0.065   6326  Z= 0.237
  Angle     :  0.633   8.936   8619  Z= 0.327
  Chirality :  0.040   0.208    966
  Planarity :  0.004   0.067   1048
  Dihedral  : 13.973  87.674   2277
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -3.12 (0.27), residues: 758
  helix: -0.96 (0.24), residues: 360
  sheet: -3.12 (0.42), residues: 99
  loop : -3.02 (0.32), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 151 
 HIS   0.001   0.000   HIS A 143 
 PHE   0.015   0.001   PHE A 311 
 TYR   0.013   0.001   TYR B 123 
 ARG   0.001   0.000   ARG B 121 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 TRP cc_start: 0.8013 (m100) cc_final: 0.7795 (m100)
REVERT: A  134 TYR cc_start: 0.7065 (t80) cc_final: 0.6847 (t80)
REVERT: A  135 MET cc_start: 0.7156 (ttm) cc_final: 0.6385 (ttm)
REVERT: A  136 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6434 (mm-30)
REVERT: A  151 TRP cc_start: 0.7689 (m100) cc_final: 0.7139 (m100)
REVERT: A  179 ILE cc_start: 0.8987 (mm) cc_final: 0.8532 (mt)
REVERT: A  234 ARG cc_start: 0.6268 (ttm-80) cc_final: 0.5843 (mtt-85)
REVERT: A  373 PHE cc_start: 0.8209 (t80) cc_final: 0.7918 (t80)
REVERT: A  408 ILE cc_start: 0.8773 (mt) cc_final: 0.8554 (mt)
REVERT: A  494 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6481 (mm-30)
REVERT: A  553 ILE cc_start: 0.9053 (pt) cc_final: 0.8831 (pt)
REVERT: C   47 GLN cc_start: 0.7619 (tm-30) cc_final: 0.7393 (tm-30)
REVERT: C   67 LEU cc_start: 0.6982 (mm) cc_final: 0.6741 (mm)
REVERT: C  114 ILE cc_start: 0.8801 (pt) cc_final: 0.8581 (mp)
REVERT: B   42 LYS cc_start: 0.6139 (mttt) cc_final: 0.5449 (tptt)
REVERT: B   53 MET cc_start: 0.8867 (tpp) cc_final: 0.8515 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.1732
  time to fit residues: 47.1211
Evaluate side-chains
  148 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0050
   chunk 30 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0870
   chunk 22 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 43 optimal weight:    9.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    0.5372

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.184878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.168277 restraints weight = 10894.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.171658 restraints weight = 6632.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.174773 restraints weight = 4690.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.4161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6901
moved from start:          0.2046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6326  Z= 0.172
  Angle     :  0.622  10.165   8619  Z= 0.311
  Chirality :  0.041   0.245    966
  Planarity :  0.004   0.072   1048
  Dihedral  :  7.263  77.856    961
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.23 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -1.75 (0.30), residues: 758
  helix:  0.26 (0.26), residues: 363
  sheet: -2.56 (0.46), residues: 100
  loop : -2.44 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 220 
 HIS   0.004   0.001   HIS C 111 
 PHE   0.018   0.001   PHE A 423 
 TYR   0.019   0.001   TYR B 123 
 ARG   0.005   0.000   ARG C 116 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 168
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6419 (mm-30)
REVERT: A  151 TRP cc_start: 0.7740 (m100) cc_final: 0.7085 (m100)
REVERT: A  240 HIS cc_start: 0.6992 (p90) cc_final: 0.6651 (m170)
REVERT: A  373 PHE cc_start: 0.8284 (t80) cc_final: 0.7827 (t80)
REVERT: A  388 GLU cc_start: 0.6767 (tm-30) cc_final: 0.6498 (tm-30)
REVERT: A  417 MET cc_start: 0.6414 (mtm) cc_final: 0.6025 (mtm)
REVERT: A  494 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6498 (mm-30)
REVERT: A  553 ILE cc_start: 0.9063 (pt) cc_final: 0.8863 (pt)
REVERT: B   42 LYS cc_start: 0.6265 (mttt) cc_final: 0.5808 (tptt)
REVERT: B   53 MET cc_start: 0.8987 (tpp) cc_final: 0.8762 (tpt)
  outliers start: 16
  outliers final: 8
  residues processed: 170
  average time/residue: 0.1642
  time to fit residues: 37.6256
Evaluate side-chains
  148 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 140
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain B residue   79 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   chunk 12 optimal weight:    5.9990
   chunk 61 optimal weight:    8.9990
   chunk 70 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 49 optimal weight:    0.1980
   chunk 21 optimal weight:    0.8980
   chunk 43 optimal weight:    7.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 ASN
** C  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  24 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.185493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.168662 restraints weight = 10989.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.172525 restraints weight = 6746.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.174297 restraints weight = 4597.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.4151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6923
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6326  Z= 0.175
  Angle     :  0.621  11.658   8619  Z= 0.309
  Chirality :  0.041   0.221    966
  Planarity :  0.004   0.072   1048
  Dihedral  :  7.081  76.811    961
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 20.46 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -1.13 (0.31), residues: 758
  helix:  0.82 (0.27), residues: 353
  sheet: -2.45 (0.47), residues: 96
  loop : -2.03 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 220 
 HIS   0.004   0.001   HIS C 111 
 PHE   0.019   0.001   PHE A 423 
 TYR   0.019   0.001   TYR A 134 
 ARG   0.002   0.000   ARG A 234 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 148
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6595 (mm-30)
REVERT: A  151 TRP cc_start: 0.7846 (m100) cc_final: 0.7251 (m100)
REVERT: A  494 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6431 (mm-30)
REVERT: A  553 ILE cc_start: 0.9096 (pt) cc_final: 0.8857 (pt)
REVERT: B   42 LYS cc_start: 0.6161 (mttt) cc_final: 0.5762 (tptt)
  outliers start: 13
  outliers final: 10
  residues processed: 153
  average time/residue: 0.1601
  time to fit residues: 33.8971
Evaluate side-chains
  145 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 135
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  311 PHE
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain C residue  111 HIS
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain B residue   79 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 2 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 55 optimal weight:    7.9990
   chunk 57 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 562 GLN
C  57 GLN
B  24 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.178727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.162076 restraints weight = 11245.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.165821 restraints weight = 6813.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.167525 restraints weight = 4664.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.4081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7054
moved from start:          0.2900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   6326  Z= 0.258
  Angle     :  0.663  10.171   8619  Z= 0.335
  Chirality :  0.043   0.193    966
  Planarity :  0.004   0.073   1048
  Dihedral  :  7.353  78.913    961
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 14.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 22.00 %
    Favored  : 74.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.30), residues: 758
  helix:  0.66 (0.27), residues: 356
  sheet: -2.57 (0.46), residues: 96
  loop : -1.92 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B  55 
 HIS   0.005   0.001   HIS C 111 
 PHE   0.023   0.002   PHE A 521 
 TYR   0.030   0.002   TYR A 134 
 ARG   0.007   0.000   ARG C  81 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 135
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6709 (mm-30)
REVERT: A  492 LEU cc_start: 0.8256 (mt) cc_final: 0.7988 (mt)
REVERT: A  494 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6635 (mm-30)
REVERT: A  553 ILE cc_start: 0.9149 (pt) cc_final: 0.8902 (pt)
REVERT: B   42 LYS cc_start: 0.6118 (mttt) cc_final: 0.5779 (tptt)
  outliers start: 25
  outliers final: 20
  residues processed: 147
  average time/residue: 0.1578
  time to fit residues: 32.0298
Evaluate side-chains
  153 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  611 SER
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue  111 HIS
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   79 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 64 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9990
   chunk 70 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 9 optimal weight:    7.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 562 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.184925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.167644 restraints weight = 10776.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.170899 restraints weight = 6612.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.174033 restraints weight = 4754.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.4156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7004
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6326  Z= 0.201
  Angle     :  0.636  11.491   8619  Z= 0.319
  Chirality :  0.042   0.272    966
  Planarity :  0.004   0.073   1048
  Dihedral  :  7.464  79.457    961
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 14.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 23.54 %
    Favored  : 72.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -1.09 (0.30), residues: 758
  helix:  0.73 (0.27), residues: 356
  sheet: -2.30 (0.47), residues: 96
  loop : -1.92 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 103 
 HIS   0.004   0.001   HIS C 111 
 PHE   0.017   0.001   PHE A 521 
 TYR   0.024   0.001   TYR A 134 
 ARG   0.003   0.000   ARG A 241 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 138
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6798 (mm-30)
REVERT: A  240 HIS cc_start: 0.6948 (p90) cc_final: 0.6731 (m170)
REVERT: A  492 LEU cc_start: 0.8216 (mt) cc_final: 0.7948 (mt)
REVERT: A  494 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6544 (mm-30)
REVERT: A  553 ILE cc_start: 0.9154 (pt) cc_final: 0.8890 (pt)
REVERT: B   42 LYS cc_start: 0.6147 (mttt) cc_final: 0.5740 (tptt)
REVERT: B   58 GLN cc_start: 0.5149 (OUTLIER) cc_final: 0.4316 (tp40)
  outliers start: 23
  outliers final: 18
  residues processed: 149
  average time/residue: 0.1592
  time to fit residues: 32.3669
Evaluate side-chains
  150 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain C residue  111 HIS
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   58 GLN
Chi-restraints excluded: chain B residue   79 TYR
Chi-restraints excluded: chain B residue  136 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 53 optimal weight:    0.0970
   chunk 34 optimal weight:    0.0870
   chunk 6 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 67 optimal weight:    6.9990
   chunk 24 optimal weight:    0.0270
   chunk 26 optimal weight:    0.4980
   chunk 71 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.2614

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 HIS ** 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 = 0.4362 r_free = 0.4362 target = 0.191460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.174518 restraints weight = 10478.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.178300 restraints weight = 6451.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.181377 restraints weight = 4530.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.4231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6855
moved from start:          0.3368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   6326  Z= 0.155
  Angle     :  0.609  10.296   8619  Z= 0.304
  Chirality :  0.041   0.319    966
  Planarity :  0.004   0.072   1048
  Dihedral  :  6.885  73.774    961
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 24.62 %
    Favored  : 72.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -0.85 (0.31), residues: 758
  helix:  0.82 (0.27), residues: 357
  sheet: -1.89 (0.47), residues: 100
  loop : -1.77 (0.37), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 103 
 HIS   0.003   0.001   HIS C 111 
 PHE   0.018   0.001   PHE A 423 
 TYR   0.019   0.001   TYR A 134 
 ARG   0.006   0.000   ARG C  81 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 144
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6690 (mm-30)
REVERT: A  151 TRP cc_start: 0.7799 (m100) cc_final: 0.7212 (m100)
REVERT: A  475 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7987 (m-80)
REVERT: A  494 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6425 (mm-30)
REVERT: A  553 ILE cc_start: 0.9139 (pt) cc_final: 0.8873 (pt)
REVERT: C   74 ARG cc_start: 0.6770 (ptt-90) cc_final: 0.6510 (ptp90)
REVERT: B   42 LYS cc_start: 0.6062 (mttt) cc_final: 0.5838 (tptt)
REVERT: B   58 GLN cc_start: 0.5042 (OUTLIER) cc_final: 0.4163 (tp40)
  outliers start: 21
  outliers final: 14
  residues processed: 154
  average time/residue: 0.1552
  time to fit residues: 32.7930
Evaluate side-chains
  148 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue  111 HIS
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   58 GLN
Chi-restraints excluded: chain B residue   79 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 50 optimal weight:    0.6980
   chunk 65 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9980
   chunk 59 optimal weight:   10.0000
   chunk 71 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 57 optimal weight:    4.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 223 HIS
A 520 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.188457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.171098 restraints weight = 10806.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.175133 restraints weight = 6713.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.178142 restraints weight = 4506.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.4203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6918
moved from start:          0.3533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6326  Z= 0.185
  Angle     :  0.662  13.213   8619  Z= 0.324
  Chirality :  0.043   0.329    966
  Planarity :  0.004   0.072   1048
  Dihedral  :  6.545  74.220    961
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 25.38 %
    Favored  : 71.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -0.75 (0.31), residues: 758
  helix:  0.89 (0.27), residues: 356
  sheet: -1.72 (0.49), residues: 96
  loop : -1.73 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 103 
 HIS   0.004   0.001   HIS C 111 
 PHE   0.013   0.001   PHE A 428 
 TYR   0.025   0.002   TYR A 134 
 ARG   0.004   0.000   ARG C  81 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 0.689 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6762 (mm-30)
REVERT: A  417 MET cc_start: 0.6284 (mtm) cc_final: 0.5978 (mtm)
REVERT: A  475 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7990 (m-80)
REVERT: A  494 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6474 (mm-30)
REVERT: A  553 ILE cc_start: 0.9135 (pt) cc_final: 0.8887 (pt)
REVERT: C   31 MET cc_start: 0.6346 (ppp) cc_final: 0.6002 (tmm)
REVERT: C   74 ARG cc_start: 0.6836 (ptt-90) cc_final: 0.6542 (ptp90)
REVERT: B   42 LYS cc_start: 0.6135 (mttt) cc_final: 0.5912 (tptt)
REVERT: B   58 GLN cc_start: 0.4995 (OUTLIER) cc_final: 0.4171 (tp40)
  outliers start: 20
  outliers final: 15
  residues processed: 149
  average time/residue: 0.1526
  time to fit residues: 31.3538
Evaluate side-chains
  156 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 139
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue  111 HIS
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   58 GLN
Chi-restraints excluded: chain B residue   79 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 9 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 16 optimal weight:    0.4980
   chunk 28 optimal weight:    2.9990
   chunk 59 optimal weight:    9.9990
   chunk 38 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 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 = 0.4334 r_free = 0.4334 target = 0.188064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.171663 restraints weight = 10325.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.175301 restraints weight = 6403.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 16)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.176564 restraints weight = 4313.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.4200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6980
moved from start:          0.3604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6326  Z= 0.208
  Angle     :  0.676  11.718   8619  Z= 0.335
  Chirality :  0.043   0.312    966
  Planarity :  0.004   0.074   1048
  Dihedral  :  6.375  75.397    961
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 14.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 25.54 %
    Favored  : 71.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -0.76 (0.31), residues: 758
  helix:  0.88 (0.27), residues: 355
  sheet: -1.79 (0.47), residues: 96
  loop : -1.70 (0.36), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 103 
 HIS   0.005   0.001   HIS C 111 
 PHE   0.025   0.002   PHE A 440 
 TYR   0.021   0.002   TYR A 134 
 ARG   0.003   0.000   ARG C  81 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6775 (mm-30)
REVERT: A  180 MET cc_start: 0.8020 (mmp) cc_final: 0.7570 (mmm)
REVERT: A  417 MET cc_start: 0.6322 (OUTLIER) cc_final: 0.6014 (mtm)
REVERT: A  494 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6517 (mm-30)
REVERT: A  553 ILE cc_start: 0.9144 (pt) cc_final: 0.8896 (pt)
REVERT: C   31 MET cc_start: 0.6381 (ppp) cc_final: 0.6122 (tmm)
REVERT: C   74 ARG cc_start: 0.6839 (ptt-90) cc_final: 0.6524 (ptp90)
REVERT: C   81 ARG cc_start: 0.3148 (tpm170) cc_final: 0.2685 (ttt-90)
REVERT: B   42 LYS cc_start: 0.6177 (mttt) cc_final: 0.5908 (tptt)
REVERT: B   58 GLN cc_start: 0.4984 (OUTLIER) cc_final: 0.4178 (tp40)
  outliers start: 22
  outliers final: 18
  residues processed: 155
  average time/residue: 0.1634
  time to fit residues: 34.4838
Evaluate side-chains
  153 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  417 MET
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   58 GLN
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   79 TYR
Chi-restraints excluded: chain B residue  136 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 45 optimal weight:    0.0570
   chunk 50 optimal weight:    6.9990
   chunk 61 optimal weight:   10.0000
   chunk 39 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.8102

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 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 = 0.4329 r_free = 0.4329 target = 0.187685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.169864 restraints weight = 10728.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.172861 restraints weight = 6481.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.176770 restraints weight = 4647.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.4189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6940
moved from start:          0.3717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6326  Z= 0.178
  Angle     :  0.666  11.483   8619  Z= 0.328
  Chirality :  0.042   0.300    966
  Planarity :  0.004   0.074   1048
  Dihedral  :  6.177  75.725    961
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 26.62 %
    Favored  : 70.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -0.66 (0.30), residues: 758
  helix:  0.92 (0.27), residues: 355
  sheet: -1.55 (0.48), residues: 95
  loop : -1.66 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 103 
 HIS   0.004   0.001   HIS C 111 
 PHE   0.022   0.001   PHE A 311 
 TYR   0.021   0.001   TYR B 123 
 ARG   0.002   0.000   ARG C  81 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6824 (mm-30)
REVERT: A  180 MET cc_start: 0.8017 (mmp) cc_final: 0.7575 (mmm)
REVERT: A  417 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.5852 (mtm)
REVERT: A  475 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.8044 (m-80)
REVERT: A  494 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6470 (mm-30)
REVERT: A  553 ILE cc_start: 0.9145 (pt) cc_final: 0.8893 (pt)
REVERT: C   74 ARG cc_start: 0.6718 (ptt-90) cc_final: 0.6402 (ptp90)
REVERT: B   42 LYS cc_start: 0.6190 (mttt) cc_final: 0.5907 (tptt)
REVERT: B   58 GLN cc_start: 0.4816 (OUTLIER) cc_final: 0.4012 (tp40)
  outliers start: 18
  outliers final: 15
  residues processed: 149
  average time/residue: 0.1789
  time to fit residues: 37.1415
Evaluate side-chains
  155 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  417 MET
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   58 GLN
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   79 TYR
Chi-restraints excluded: chain B residue  136 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 8 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0070
   chunk 51 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 17 optimal weight:   10.0000
   chunk 7 optimal weight:    4.9990
   overall best weight:    0.9200

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 416 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.187626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.170700 restraints weight = 10908.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.174430 restraints weight = 6765.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.177415 restraints weight = 4531.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.4211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6925
moved from start:          0.3802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6326  Z= 0.190
  Angle     :  0.675  11.234   8619  Z= 0.333
  Chirality :  0.042   0.286    966
  Planarity :  0.004   0.074   1048
  Dihedral  :  6.085  74.907    961
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 26.92 %
    Favored  : 70.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.30), residues: 758
  helix:  0.91 (0.27), residues: 354
  sheet: -1.51 (0.48), residues: 95
  loop : -1.60 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 103 
 HIS   0.004   0.001   HIS C 111 
 PHE   0.024   0.001   PHE A 311 
 TYR   0.022   0.002   TYR B 123 
 ARG   0.012   0.000   ARG C  81 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6746 (mm-30)
REVERT: A  180 MET cc_start: 0.7982 (mmp) cc_final: 0.7551 (mmm)
REVERT: A  417 MET cc_start: 0.6246 (OUTLIER) cc_final: 0.5805 (mtm)
REVERT: A  475 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7959 (m-80)
REVERT: A  494 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6477 (mm-30)
REVERT: A  553 ILE cc_start: 0.9123 (pt) cc_final: 0.8877 (pt)
REVERT: C   74 ARG cc_start: 0.6757 (ptt-90) cc_final: 0.6470 (ptp90)
REVERT: B   58 GLN cc_start: 0.4795 (OUTLIER) cc_final: 0.4034 (tp40)
  outliers start: 18
  outliers final: 15
  residues processed: 145
  average time/residue: 0.1683
  time to fit residues: 33.9674
Evaluate side-chains
  152 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  391 ASN
Chi-restraints excluded: chain A residue  417 MET
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   58 GLN
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   79 TYR
Chi-restraints excluded: chain B residue  136 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 55 optimal weight:    8.9990
   chunk 47 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 61 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 63 optimal weight:    3.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 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 = 0.4336 r_free = 0.4336 target = 0.188758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.171351 restraints weight = 11122.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.175076 restraints weight = 6910.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.178137 restraints weight = 4776.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.4215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6910
moved from start:          0.3936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6326  Z= 0.185
  Angle     :  0.685  11.730   8619  Z= 0.334
  Chirality :  0.042   0.280    966
  Planarity :  0.004   0.074   1048
  Dihedral  :  5.998  74.488    961
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 26.92 %
    Favored  : 70.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -0.56 (0.30), residues: 758
  helix:  0.90 (0.27), residues: 354
  sheet: -1.47 (0.49), residues: 95
  loop : -1.48 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 541 
 HIS   0.004   0.001   HIS C 111 
 PHE   0.025   0.001   PHE A 311 
 TYR   0.020   0.001   TYR B 123 
 ARG   0.007   0.000   ARG C  81 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2216.13 seconds
wall clock time: 40 minutes 33.98 seconds (2433.98 seconds total)