Starting phenix.real_space_refine
on Tue Jan 14 06:56:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rbg_19031/01_2025/8rbg_19031.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rbg_19031/01_2025/8rbg_19031.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rbg_19031/01_2025/8rbg_19031.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rbg_19031/01_2025/8rbg_19031.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rbg_19031/01_2025/8rbg_19031.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rbg_19031/01_2025/8rbg_19031.cif"
  }
  resolution = 4.9
  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=   0.038
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      35      5.16       5
     C    3835      2.51       5
     N    1024      2.21       5
     O    1110      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 6008
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5975
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 737, 5975
          Classifications: {'peptide': 737}
          Link IDs: {'PTRANS': 26, 'TRANS': 710}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 3.80, per 1000 atoms: 0.63
  Number of scatterers: 6008
  At special positions: 0
  Unit cell: (111.28, 83.46, 92.02, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      35     16.00
     P       3     15.00
     Mg      1     11.99
     O    1110      8.00
     N    1024      7.00
     C    3835      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.69
  Conformation dependent library (CDL) restraints added in 911.0 milliseconds
  

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1400

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 7 sheets defined
      56.6% alpha, 12.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 7
    Processing helix  chain 'A' and resid 65 through 69
    Processing helix  chain 'A' and resid 73 through 77
    Processing helix  chain 'A' and resid 81 through 95
    Processing helix  chain 'A' and resid 120 through 128
    Processing helix  chain 'A' and resid 138 through 154
      removed outlier: 3.674A  pdb=" N   VAL A 142 " --> pdb=" O   HIS A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 185
    Processing helix  chain 'A' and resid 190 through 207
      removed outlier: 4.175A  pdb=" N   ASN A 200 " --> pdb=" O   VAL A 196 " (cutoff:3.500A)
      Proline residue:  A 201  - end of helix
    Processing helix  chain 'A' and resid 246 through 251
      removed outlier: 4.248A  pdb=" N   VAL A 250 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 268
      removed outlier: 4.128A  pdb=" N   TYR A 263 " --> pdb=" O   TYR A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 278
      removed outlier: 4.500A  pdb=" N   MET A 276 " --> pdb=" O   GLU A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 284
    Processing helix  chain 'A' and resid 285 through 290
    Processing helix  chain 'A' and resid 300 through 316
    Processing helix  chain 'A' and resid 318 through 337
      removed outlier: 3.650A  pdb=" N   ASN A 337 " --> pdb=" O   LEU A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 365
    Processing helix  chain 'A' and resid 367 through 376
    Processing helix  chain 'A' and resid 392 through 424
    Processing helix  chain 'A' and resid 448 through 470
    Processing helix  chain 'A' and resid 470 through 481
      removed outlier: 3.576A  pdb=" N   TYR A 477 " --> pdb=" O   GLU A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 501
    Processing helix  chain 'A' and resid 504 through 515
      removed outlier: 3.518A  pdb=" N   MET A 515 " --> pdb=" O   GLU A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 532
    Processing helix  chain 'A' and resid 563 through 570
    Processing helix  chain 'A' and resid 573 through 582
    Processing helix  chain 'A' and resid 586 through 593
    Processing helix  chain 'A' and resid 634 through 653
      removed outlier: 3.998A  pdb=" N   THR A 653 " --> pdb=" O   THR A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 685
      removed outlier: 3.554A  pdb=" N   GLN A 680 " --> pdb=" O   ARG A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 685 through 696
      removed outlier: 3.521A  pdb=" N   GLY A 696 " --> pdb=" O   ILE A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 711
    Processing helix  chain 'A' and resid 712 through 714
      No H-bonds generated for 'chain 'A' and resid 712 through 714'
    Processing helix  chain 'A' and resid 715 through 719
    Processing helix  chain 'A' and resid 722 through 735
    Processing helix  chain 'A' and resid 737 through 739
      No H-bonds generated for 'chain 'A' and resid 737 through 739'
    Processing helix  chain 'A' and resid 753 through 778
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 51
      removed outlier: 3.542A  pdb=" N   HIS A  61 " --> pdb=" O   TRP A  14 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 103
      removed outlier: 3.684A  pdb=" N   VAL A 106 " --> pdb=" O   CYS A 103 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   LEU A 107 " --> pdb=" O   ARG A 659 " (cutoff:3.500A)
      removed outlier: 7.817A  pdb=" N   ILE A 661 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   ALA A 109 " --> pdb=" O   ILE A 661 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   SER A 158 " --> pdb=" O   HIS A 656 " (cutoff:3.500A)
      removed outlier: 7.619A  pdb=" N   VAL A 658 " --> pdb=" O   SER A 158 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ILE A 160 " --> pdb=" O   VAL A 658 " (cutoff:3.500A)
      removed outlier: 7.600A  pdb=" N   CYS A 660 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   SER A 162 " --> pdb=" O   CYS A 660 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   VAL A 161 " --> pdb=" O   LEU A 436 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLY A 236 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 209
    Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 343
    Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 381
    Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 539
    Processing sheet with id=AA7, first strand: chain 'A' and resid 699 through 702
      removed outlier: 4.490A  pdb=" N   SER A 699 " --> pdb=" O   PHE A 750 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   PHE A 750 " --> pdb=" O   SER A 699 " (cutoff:3.500A)

    326 hydrogen bonds defined for protein.
    915 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.92

  Time building geometry restraints manager: 1.91 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1508
        1.33 -     1.45: 1245
        1.45 -     1.58: 3333
        1.58 -     1.70: 1
        1.70 -     1.82: 54
  Bond restraints: 6141
  Sorted by residual:
  bond pdb=" C4  ADP A 903 "
       pdb=" C5  ADP A 903 "
    ideal  model  delta    sigma   weight residual
    1.490  1.380  0.110 2.00e-02 2.50e+03 3.03e+01
  bond pdb=" C5  ADP A 903 "
       pdb=" C6  ADP A 903 "
    ideal  model  delta    sigma   weight residual
    1.490  1.406  0.084 2.00e-02 2.50e+03 1.75e+01
  bond pdb=" O4  PO4 A 901 "
       pdb=" P   PO4 A 901 "
    ideal  model  delta    sigma   weight residual
    1.568  1.486  0.082 2.00e-02 2.50e+03 1.68e+01
  bond pdb=" O3  PO4 A 901 "
       pdb=" P   PO4 A 901 "
    ideal  model  delta    sigma   weight residual
    1.569  1.495  0.074 2.00e-02 2.50e+03 1.38e+01
  bond pdb=" CZ  ARG A 676 "
       pdb=" NH2 ARG A 676 "
    ideal  model  delta    sigma   weight residual
    1.330  1.285  0.045 1.30e-02 5.92e+03 1.20e+01
  ... (remaining 6136 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 6459
        2.19 -     4.39: 1554
        4.39 -     6.58: 231
        6.58 -     8.78: 33
        8.78 -    10.97: 9
  Bond angle restraints: 8286
  Sorted by residual:
  angle pdb=" C   THR A 170 "
        pdb=" N   VAL A 171 "
        pdb=" CA  VAL A 171 "
      ideal   model   delta    sigma   weight residual
     120.56  130.61  -10.05 1.26e+00 6.30e-01 6.36e+01
  angle pdb=" CA  PRO A 589 "
        pdb=" N   PRO A 589 "
        pdb=" CD  PRO A 589 "
      ideal   model   delta    sigma   weight residual
     112.00  101.03   10.97 1.40e+00 5.10e-01 6.14e+01
  angle pdb=" N   GLU A 500 "
        pdb=" CA  GLU A 500 "
        pdb=" C   GLU A 500 "
      ideal   model   delta    sigma   weight residual
     112.23  119.86   -7.63 1.26e+00 6.30e-01 3.67e+01
  angle pdb=" CA  HIS A 418 "
        pdb=" CB  HIS A 418 "
        pdb=" CG  HIS A 418 "
      ideal   model   delta    sigma   weight residual
     113.80  108.16    5.64 1.00e+00 1.00e+00 3.18e+01
  angle pdb=" N   GLU A 254 "
        pdb=" CA  GLU A 254 "
        pdb=" C   GLU A 254 "
      ideal   model   delta    sigma   weight residual
     112.34  119.66   -7.32 1.30e+00 5.92e-01 3.17e+01
  ... (remaining 8281 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.56: 3638
       31.56 -    63.12: 61
       63.12 -    94.67: 7
       94.67 -   126.23: 1
      126.23 -   157.79: 1
  Dihedral angle restraints: 3708
    sinusoidal: 1540
      harmonic: 2168
  Sorted by residual:
  dihedral pdb=" O1B ADP A 903 "
           pdb=" O3A ADP A 903 "
           pdb=" PB  ADP A 903 "
           pdb=" PA  ADP A 903 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   97.78 -157.79     1      2.00e+01 2.50e-03 4.62e+01
  dihedral pdb=" C5' ADP A 903 "
           pdb=" O5' ADP A 903 "
           pdb=" PA  ADP A 903 "
           pdb=" O2A ADP A 903 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -169.90  109.90     1      2.00e+01 2.50e-03 3.22e+01
  dihedral pdb=" C   GLU A 154 "
           pdb=" N   GLU A 154 "
           pdb=" CA  GLU A 154 "
           pdb=" CB  GLU A 154 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.79   13.19     0      2.50e+00 1.60e-01 2.78e+01
  ... (remaining 3705 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 565
       0.092 -    0.184: 258
       0.184 -    0.277: 53
       0.277 -    0.369: 13
       0.369 -    0.461: 3
  Chirality restraints: 892
  Sorted by residual:
  chirality pdb=" CA  LYS A 169 "
            pdb=" N   LYS A 169 "
            pdb=" C   LYS A 169 "
            pdb=" CB  LYS A 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.31e+00
  chirality pdb=" CA  GLN A 474 "
            pdb=" N   GLN A 474 "
            pdb=" C   GLN A 474 "
            pdb=" CB  GLN A 474 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.77e+00
  chirality pdb=" CA  GLU A 154 "
            pdb=" N   GLU A 154 "
            pdb=" C   GLU A 154 "
            pdb=" CB  GLU A 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.53e+00
  ... (remaining 889 not shown)

  Planarity restraints: 1060
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 232 "   -0.146 2.00e-02 2.50e+03   7.88e-02 1.24e+02
        pdb=" CG  TYR A 232 "    0.055 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 232 "    0.066 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 232 "    0.055 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 232 "    0.038 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 232 "    0.047 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 232 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 232 "   -0.119 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 223 "    0.109 2.00e-02 2.50e+03   7.63e-02 1.16e+02
        pdb=" CG  TYR A 223 "    0.013 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 223 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 223 "   -0.062 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 223 "   -0.080 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 223 "   -0.054 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 223 "   -0.021 2.00e-02 2.50e+03
        pdb=" OH  TYR A 223 "    0.138 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 439 "   -0.105 2.00e-02 2.50e+03   6.63e-02 8.79e+01
        pdb=" CG  TYR A 439 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 439 "    0.073 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 439 "    0.044 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 439 "    0.030 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 439 "    0.070 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 439 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR A 439 "   -0.105 2.00e-02 2.50e+03
  ... (remaining 1057 not shown)

  Histogram of nonbonded interaction distances:
        1.82 -     2.44: 9
        2.44 -     3.05: 3632
        3.05 -     3.67: 8979
        3.67 -     4.28: 13370
        4.28 -     4.90: 21878
  Nonbonded interactions: 47868
  Sorted by model distance:
  nonbonded pdb=" O1  PO4 A 901 "
            pdb="MG    MG A 902 "
     model   vdw
     1.819 2.170
  nonbonded pdb=" CD  ARG A 343 "
            pdb=" OG1 THR A 349 "
     model   vdw
     2.043 3.440
  nonbonded pdb="MG    MG A 902 "
            pdb=" O1B ADP A 903 "
     model   vdw
     2.132 2.170
  nonbonded pdb=" OG1 THR A 170 "
            pdb="MG    MG A 902 "
     model   vdw
     2.159 2.170
  nonbonded pdb=" CG2 VAL A 106 "
            pdb=" NH1 ARG A 659 "
     model   vdw
     2.227 3.540
  ... (remaining 47863 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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=0.50 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:             0.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     18.030
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6766
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      :  0.013   0.110   6141  Z= 0.824
  Angle     :  1.922  10.971   8286  Z= 1.261
  Chirality :  0.107   0.461    892
  Planarity :  0.019   0.281   1060
  Dihedral  : 12.429 157.788   2308
  Min Nonbonded Distance : 1.819

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  2.73 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  0.31 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.71 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.29), residues: 733
  helix:  1.19 (0.25), residues: 359
  sheet:  0.38 (0.50), residues: 87
  loop : -0.52 (0.34), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.072   0.022   TRP A 484 
 HIS   0.014   0.004   HIS A 644 
 PHE   0.096   0.017   PHE A 666 
 TYR   0.146   0.029   TYR A 232 
 ARG   0.019   0.002   ARG A 676 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 227
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 PHE cc_start: 0.7495 (m-10) cc_final: 0.7282 (m-80)
REVERT: A  169 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7508 (pttm)
REVERT: A  180 PHE cc_start: 0.7791 (m-80) cc_final: 0.7568 (m-80)
REVERT: A  216 ASN cc_start: 0.8230 (t0) cc_final: 0.7737 (t0)
REVERT: A  220 PHE cc_start: 0.8255 (p90) cc_final: 0.7891 (p90)
REVERT: A  258 ASN cc_start: 0.7492 (t0) cc_final: 0.7071 (t0)
REVERT: A  262 PHE cc_start: 0.8543 (m-80) cc_final: 0.8033 (m-80)
REVERT: A  296 ILE cc_start: 0.7732 (mt) cc_final: 0.7386 (mm)
REVERT: A  299 VAL cc_start: 0.6230 (t) cc_final: 0.5971 (t)
REVERT: A  416 VAL cc_start: 0.8949 (m) cc_final: 0.8731 (m)
REVERT: A  420 ASN cc_start: 0.8556 (m110) cc_final: 0.8082 (m110)
REVERT: A  439 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.7808 (p90)
REVERT: A  509 LEU cc_start: 0.8934 (tp) cc_final: 0.7929 (tp)
REVERT: A  552 HIS cc_start: 0.7681 (m-70) cc_final: 0.7480 (m90)
REVERT: A  559 TYR cc_start: 0.7804 (m-80) cc_final: 0.7130 (m-80)
  outliers start: 4
  outliers final: 2
  residues processed: 230
  average time/residue: 0.2563
  time to fit residues: 71.3795
Evaluate side-chains
  143 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 139
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 61 optimal weight:    0.0970
   chunk 55 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
A  87 HIS
** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 260 HIS
** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 420 ASN
** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 429 GLN
A 463 GLN
A 531 HIS
A 576 GLN
A 637 HIS
** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.086422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.054369 restraints weight = 25379.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.056507 restraints weight = 18312.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.058090 restraints weight = 14301.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3187
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3184
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.4700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6141  Z= 0.214
  Angle     :  0.680   7.456   8286  Z= 0.366
  Chirality :  0.042   0.192    892
  Planarity :  0.005   0.079   1060
  Dihedral  :  7.278 128.923    814
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.48 %
    Favored  : 97.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.31), residues: 733
  helix:  1.66 (0.27), residues: 365
  sheet: -0.06 (0.45), residues: 104
  loop : -0.16 (0.40), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 523 
 HIS   0.008   0.002   HIS A 286 
 PHE   0.039   0.002   PHE A 360 
 TYR   0.030   0.003   TYR A 368 
 ARG   0.004   0.001   ARG A 640 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 168
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 ASN cc_start: 0.8735 (t0) cc_final: 0.7846 (t0)
REVERT: A  262 PHE cc_start: 0.9434 (m-80) cc_final: 0.8612 (m-80)
REVERT: A  304 GLU cc_start: 0.8759 (mp0) cc_final: 0.8363 (mp0)
REVERT: A  326 PHE cc_start: 0.9358 (m-80) cc_final: 0.9053 (m-80)
REVERT: A  360 PHE cc_start: 0.9413 (t80) cc_final: 0.8977 (t80)
REVERT: A  371 MET cc_start: 0.9431 (mtm) cc_final: 0.8993 (mtt)
REVERT: A  387 TYR cc_start: 0.8605 (t80) cc_final: 0.8286 (t80)
REVERT: A  408 TYR cc_start: 0.8707 (t80) cc_final: 0.8161 (t80)
REVERT: A  410 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8657 (mttt)
REVERT: A  438 ILE cc_start: 0.9061 (mm) cc_final: 0.8764 (mm)
REVERT: A  439 TYR cc_start: 0.8885 (p90) cc_final: 0.8448 (p90)
REVERT: A  460 LYS cc_start: 0.9795 (tptt) cc_final: 0.9480 (tptp)
REVERT: A  527 LEU cc_start: 0.9692 (mt) cc_final: 0.9441 (mt)
REVERT: A  557 VAL cc_start: 0.9301 (t) cc_final: 0.8814 (t)
REVERT: A  559 TYR cc_start: 0.8424 (m-80) cc_final: 0.7090 (m-80)
REVERT: A  564 PHE cc_start: 0.9611 (m-80) cc_final: 0.8978 (m-80)
REVERT: A  580 LEU cc_start: 0.9289 (mm) cc_final: 0.8914 (pp)
REVERT: A  648 GLU cc_start: 0.9604 (mt-10) cc_final: 0.9395 (mt-10)
REVERT: A  701 TRP cc_start: 0.9554 (m-90) cc_final: 0.9150 (m-90)
REVERT: A  710 TYR cc_start: 0.8165 (m-80) cc_final: 0.7813 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 169
  average time/residue: 0.2348
  time to fit residues: 49.4648
Evaluate side-chains
  125 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 33 optimal weight:    0.8980
   chunk 52 optimal weight:    6.9990
   chunk 16 optimal weight:    0.0370
   chunk 9 optimal weight:    5.9990
   chunk 71 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 47 optimal weight:    6.9990
   chunk 72 optimal weight:   20.0000
   chunk 50 optimal weight:    6.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.6658

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

Flipped N/Q/H residues before XYZ refinement:
** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 552 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 = 0.3706 r_free = 0.3706 target = 0.085602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.054372 restraints weight = 25996.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.056492 restraints weight = 18700.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.058109 restraints weight = 14624.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3183
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3183 r_free = 0.3183    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3182
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.5601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6141  Z= 0.168
  Angle     :  0.616   6.654   8286  Z= 0.325
  Chirality :  0.041   0.158    892
  Planarity :  0.005   0.064   1060
  Dihedral  :  7.043 131.148    814
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.17 %
    Favored  : 97.67 %
  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:  1.18 (0.31), residues: 733
  helix:  1.69 (0.27), residues: 367
  sheet:  0.22 (0.47), residues: 103
  loop : -0.20 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 414 
 HIS   0.007   0.001   HIS A 468 
 PHE   0.026   0.002   PHE A 360 
 TYR   0.016   0.002   TYR A 259 
 ARG   0.005   0.001   ARG A 327 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 161
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 ARG cc_start: 0.9585 (tpt170) cc_final: 0.9282 (tpp80)
REVERT: A  140 PHE cc_start: 0.8707 (m-80) cc_final: 0.8085 (m-80)
REVERT: A  258 ASN cc_start: 0.8461 (t0) cc_final: 0.7526 (t0)
REVERT: A  262 PHE cc_start: 0.9426 (m-80) cc_final: 0.8646 (m-80)
REVERT: A  275 LYS cc_start: 0.9549 (mmmt) cc_final: 0.9228 (mmmt)
REVERT: A  319 GLU cc_start: 0.8593 (tp30) cc_final: 0.7547 (tp30)
REVERT: A  323 MET cc_start: 0.9464 (mmp) cc_final: 0.9058 (mmm)
REVERT: A  360 PHE cc_start: 0.9331 (t80) cc_final: 0.8839 (t80)
REVERT: A  387 TYR cc_start: 0.8589 (t80) cc_final: 0.8317 (t80)
REVERT: A  408 TYR cc_start: 0.8650 (t80) cc_final: 0.8188 (t80)
REVERT: A  438 ILE cc_start: 0.9153 (mm) cc_final: 0.8849 (mm)
REVERT: A  439 TYR cc_start: 0.8631 (p90) cc_final: 0.8429 (p90)
REVERT: A  459 GLU cc_start: 0.9432 (mm-30) cc_final: 0.9106 (mm-30)
REVERT: A  460 LYS cc_start: 0.9774 (tptt) cc_final: 0.9475 (tptp)
REVERT: A  527 LEU cc_start: 0.9647 (mt) cc_final: 0.9367 (mt)
REVERT: A  552 HIS cc_start: 0.7981 (m90) cc_final: 0.7659 (m90)
REVERT: A  557 VAL cc_start: 0.9295 (t) cc_final: 0.9030 (t)
REVERT: A  564 PHE cc_start: 0.9666 (m-80) cc_final: 0.8865 (m-80)
REVERT: A  580 LEU cc_start: 0.9298 (mm) cc_final: 0.8895 (pp)
REVERT: A  639 PHE cc_start: 0.9112 (t80) cc_final: 0.8822 (t80)
REVERT: A  676 ARG cc_start: 0.9431 (tpt90) cc_final: 0.8822 (mmm160)
REVERT: A  750 PHE cc_start: 0.8684 (m-80) cc_final: 0.7186 (m-10)
REVERT: A  755 VAL cc_start: 0.8668 (t) cc_final: 0.8356 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 162
  average time/residue: 0.2165
  time to fit residues: 44.2269
Evaluate side-chains
  118 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 34 optimal weight:    8.9990
   chunk 56 optimal weight:    6.9990
   chunk 8 optimal weight:    8.9990
   chunk 51 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 68 optimal weight:   30.0000
   chunk 6 optimal weight:    3.9990
   chunk 28 optimal weight:    0.4980
   chunk 10 optimal weight:    5.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 637 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.082324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.050974 restraints weight = 28475.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.053004 restraints weight = 20593.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.054444 restraints weight = 16090.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3102
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3102 r_free = 0.3102    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3102 r_free = 0.3102    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3102
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.6155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6141  Z= 0.201
  Angle     :  0.618   6.571   8286  Z= 0.326
  Chirality :  0.041   0.158    892
  Planarity :  0.004   0.055   1060
  Dihedral  :  7.210 133.443    814
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  1.86 %
    Favored  : 97.67 %
  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:  1.01 (0.31), residues: 733
  helix:  1.54 (0.28), residues: 365
  sheet:  0.27 (0.47), residues: 96
  loop : -0.29 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP A 523 
 HIS   0.007   0.001   HIS A 468 
 PHE   0.020   0.002   PHE A 326 
 TYR   0.019   0.002   TYR A 439 
 ARG   0.004   0.001   ARG A 219 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 146
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 ARG cc_start: 0.9600 (tpt170) cc_final: 0.9279 (tpp80)
REVERT: A  139 ILE cc_start: 0.9629 (tt) cc_final: 0.9422 (tt)
REVERT: A  140 PHE cc_start: 0.8838 (m-80) cc_final: 0.8048 (m-80)
REVERT: A  239 MET cc_start: 0.8966 (tmm) cc_final: 0.8760 (tmm)
REVERT: A  258 ASN cc_start: 0.8367 (t0) cc_final: 0.7657 (t0)
REVERT: A  262 PHE cc_start: 0.9483 (m-80) cc_final: 0.8320 (m-80)
REVERT: A  304 GLU cc_start: 0.9028 (mp0) cc_final: 0.8368 (mp0)
REVERT: A  319 GLU cc_start: 0.8608 (tp30) cc_final: 0.7610 (tp30)
REVERT: A  323 MET cc_start: 0.9458 (mmp) cc_final: 0.9076 (mmm)
REVERT: A  335 LEU cc_start: 0.9783 (tp) cc_final: 0.9571 (tp)
REVERT: A  360 PHE cc_start: 0.9256 (t80) cc_final: 0.9045 (t80)
REVERT: A  408 TYR cc_start: 0.8686 (t80) cc_final: 0.8196 (t80)
REVERT: A  438 ILE cc_start: 0.9099 (mm) cc_final: 0.8864 (mm)
REVERT: A  459 GLU cc_start: 0.9445 (mm-30) cc_final: 0.9102 (mm-30)
REVERT: A  460 LYS cc_start: 0.9780 (tptt) cc_final: 0.9495 (tptp)
REVERT: A  467 MET cc_start: 0.9472 (tmm) cc_final: 0.9253 (tmm)
REVERT: A  548 PHE cc_start: 0.9332 (p90) cc_final: 0.8802 (p90)
REVERT: A  552 HIS cc_start: 0.8230 (m90) cc_final: 0.7823 (m90)
REVERT: A  557 VAL cc_start: 0.9344 (t) cc_final: 0.9065 (t)
REVERT: A  580 LEU cc_start: 0.9206 (mm) cc_final: 0.8901 (pp)
REVERT: A  676 ARG cc_start: 0.9434 (tpt90) cc_final: 0.8820 (mmm160)
REVERT: A  700 ARG cc_start: 0.8307 (ttp80) cc_final: 0.7889 (ttp80)
REVERT: A  701 TRP cc_start: 0.9450 (m-90) cc_final: 0.8928 (m-90)
  outliers start: 3
  outliers final: 0
  residues processed: 147
  average time/residue: 0.2110
  time to fit residues: 40.0361
Evaluate side-chains
  107 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 68 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    6.9990
   chunk 65 optimal weight:    6.9990
   chunk 26 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 47 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0670
   overall best weight:    2.5722

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

Flipped N/Q/H residues before XYZ refinement:
A 191 ASN
A 200 ASN
** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.077706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.047861 restraints weight = 29575.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.049746 restraints weight = 21272.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.051113 restraints weight = 16734.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3031
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3031
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.6932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6141  Z= 0.246
  Angle     :  0.658   6.639   8286  Z= 0.347
  Chirality :  0.042   0.147    892
  Planarity :  0.005   0.050   1060
  Dihedral  :  7.477 136.232    814
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 15.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.30), residues: 733
  helix:  1.13 (0.27), residues: 360
  sheet: -0.27 (0.47), residues: 96
  loop : -0.38 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP A  22 
 HIS   0.006   0.001   HIS A  87 
 PHE   0.021   0.002   PHE A 449 
 TYR   0.020   0.002   TYR A 259 
 ARG   0.004   0.001   ARG A 219 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 ARG cc_start: 0.9593 (tpt170) cc_final: 0.9249 (tpp80)
REVERT: A  140 PHE cc_start: 0.8903 (m-80) cc_final: 0.8146 (m-80)
REVERT: A  219 ARG cc_start: 0.8610 (mmp80) cc_final: 0.8383 (mmp80)
REVERT: A  262 PHE cc_start: 0.9553 (m-80) cc_final: 0.8943 (m-80)
REVERT: A  319 GLU cc_start: 0.8435 (tp30) cc_final: 0.7376 (tp30)
REVERT: A  323 MET cc_start: 0.9550 (mmp) cc_final: 0.9206 (mmm)
REVERT: A  326 PHE cc_start: 0.9313 (m-10) cc_final: 0.8986 (m-80)
REVERT: A  360 PHE cc_start: 0.9238 (t80) cc_final: 0.9035 (t80)
REVERT: A  408 TYR cc_start: 0.8888 (t80) cc_final: 0.8626 (t80)
REVERT: A  460 LYS cc_start: 0.9770 (tptt) cc_final: 0.9480 (tptp)
REVERT: A  552 HIS cc_start: 0.8384 (m90) cc_final: 0.8178 (m90)
REVERT: A  567 LYS cc_start: 0.9728 (ptpt) cc_final: 0.9451 (pttm)
REVERT: A  676 ARG cc_start: 0.9593 (mmm160) cc_final: 0.9180 (mmm160)
REVERT: A  692 ILE cc_start: 0.9215 (pt) cc_final: 0.8984 (pt)
REVERT: A  701 TRP cc_start: 0.9194 (m-90) cc_final: 0.8208 (m-90)
REVERT: A  714 MET cc_start: 0.7300 (tpp) cc_final: 0.7051 (tpp)
REVERT: A  750 PHE cc_start: 0.9074 (m-80) cc_final: 0.8003 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.2086
  time to fit residues: 35.1189
Evaluate side-chains
  102 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 66 optimal weight:    2.9990
   chunk 48 optimal weight:    7.9990
   chunk 13 optimal weight:   20.0000
   chunk 32 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 55 optimal weight:   10.0000
   chunk 58 optimal weight:    8.9990
   chunk 46 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 290 GLN
** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 754 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.076585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.047436 restraints weight = 29901.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.049263 restraints weight = 21621.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.050622 restraints weight = 17034.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3012
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3012
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.7439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6141  Z= 0.253
  Angle     :  0.652   6.400   8286  Z= 0.343
  Chirality :  0.041   0.200    892
  Planarity :  0.004   0.045   1060
  Dihedral  :  7.487 133.219    814
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 17.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.30), residues: 733
  helix:  0.95 (0.27), residues: 361
  sheet: -0.74 (0.45), residues: 102
  loop : -0.33 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A  22 
 HIS   0.006   0.002   HIS A 552 
 PHE   0.017   0.002   PHE A 743 
 TYR   0.015   0.002   TYR A 113 
 ARG   0.004   0.001   ARG A 219 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.690 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 TRP cc_start: 0.9300 (m100) cc_final: 0.9033 (m100)
REVERT: A   92 ARG cc_start: 0.9616 (tpt170) cc_final: 0.9317 (tpp80)
REVERT: A  140 PHE cc_start: 0.8836 (m-80) cc_final: 0.8140 (m-80)
REVERT: A  262 PHE cc_start: 0.9537 (m-80) cc_final: 0.9118 (m-80)
REVERT: A  319 GLU cc_start: 0.8404 (tp30) cc_final: 0.8041 (tp30)
REVERT: A  323 MET cc_start: 0.9518 (mmp) cc_final: 0.9226 (mmp)
REVERT: A  326 PHE cc_start: 0.9293 (m-10) cc_final: 0.8690 (m-80)
REVERT: A  340 PHE cc_start: 0.7097 (p90) cc_final: 0.6658 (p90)
REVERT: A  360 PHE cc_start: 0.9197 (t80) cc_final: 0.8978 (t80)
REVERT: A  460 LYS cc_start: 0.9763 (tptt) cc_final: 0.9532 (tmtt)
REVERT: A  567 LYS cc_start: 0.9723 (ptpt) cc_final: 0.9520 (pttm)
REVERT: A  580 LEU cc_start: 0.9310 (mm) cc_final: 0.9003 (pp)
REVERT: A  588 LEU cc_start: 0.9158 (mt) cc_final: 0.8913 (mt)
REVERT: A  676 ARG cc_start: 0.9607 (mmm160) cc_final: 0.9192 (mmm160)
REVERT: A  692 ILE cc_start: 0.9126 (pt) cc_final: 0.8909 (pt)
REVERT: A  701 TRP cc_start: 0.9305 (m-90) cc_final: 0.8242 (m-90)
REVERT: A  714 MET cc_start: 0.6847 (tpp) cc_final: 0.6594 (tpp)
REVERT: A  746 THR cc_start: 0.8357 (m) cc_final: 0.8149 (p)
REVERT: A  750 PHE cc_start: 0.9195 (m-80) cc_final: 0.7977 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.2071
  time to fit residues: 36.1287
Evaluate side-chains
  107 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 59 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   chunk 13 optimal weight:   20.0000
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 200 ASN
** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 754 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.080364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.050656 restraints weight = 28697.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.052715 restraints weight = 20220.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.054263 restraints weight = 15661.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3110
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3110
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.7616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6141  Z= 0.168
  Angle     :  0.600   6.622   8286  Z= 0.318
  Chirality :  0.041   0.190    892
  Planarity :  0.004   0.041   1060
  Dihedral  :  7.195 133.018    814
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.30), residues: 733
  helix:  1.22 (0.27), residues: 361
  sheet: -0.36 (0.48), residues: 96
  loop : -0.35 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  22 
 HIS   0.006   0.001   HIS A 552 
 PHE   0.025   0.002   PHE A 639 
 TYR   0.022   0.002   TYR A 263 
 ARG   0.005   0.001   ARG A 257 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 TRP cc_start: 0.9359 (m100) cc_final: 0.8953 (m100)
REVERT: A   92 ARG cc_start: 0.9615 (tpt170) cc_final: 0.9313 (tpp80)
REVERT: A  140 PHE cc_start: 0.8785 (m-80) cc_final: 0.8159 (m-80)
REVERT: A  219 ARG cc_start: 0.8414 (mmp80) cc_final: 0.8192 (mmp80)
REVERT: A  262 PHE cc_start: 0.9582 (m-80) cc_final: 0.8993 (m-80)
REVERT: A  304 GLU cc_start: 0.9370 (mp0) cc_final: 0.8844 (mp0)
REVERT: A  319 GLU cc_start: 0.8749 (tp30) cc_final: 0.7935 (tp30)
REVERT: A  340 PHE cc_start: 0.7190 (p90) cc_final: 0.6682 (p90)
REVERT: A  360 PHE cc_start: 0.9162 (t80) cc_final: 0.8916 (t80)
REVERT: A  438 ILE cc_start: 0.8824 (mm) cc_final: 0.8609 (mm)
REVERT: A  439 TYR cc_start: 0.8364 (p90) cc_final: 0.7993 (p90)
REVERT: A  460 LYS cc_start: 0.9750 (tptt) cc_final: 0.9367 (tptp)
REVERT: A  467 MET cc_start: 0.9350 (tmm) cc_final: 0.9142 (tmm)
REVERT: A  559 TYR cc_start: 0.8194 (m-80) cc_final: 0.7589 (m-80)
REVERT: A  567 LYS cc_start: 0.9692 (ptpt) cc_final: 0.9468 (pttm)
REVERT: A  580 LEU cc_start: 0.9280 (mm) cc_final: 0.9000 (pp)
REVERT: A  588 LEU cc_start: 0.9141 (mt) cc_final: 0.8890 (mt)
REVERT: A  692 ILE cc_start: 0.9195 (pt) cc_final: 0.8962 (pt)
REVERT: A  701 TRP cc_start: 0.9358 (m-90) cc_final: 0.8466 (m-90)
REVERT: A  714 MET cc_start: 0.6796 (tpp) cc_final: 0.6415 (tpp)
REVERT: A  746 THR cc_start: 0.8350 (m) cc_final: 0.8135 (p)
REVERT: A  750 PHE cc_start: 0.9192 (m-80) cc_final: 0.7852 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.2111
  time to fit residues: 35.9156
Evaluate side-chains
  114 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 36 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 50 optimal weight:    0.3980
   chunk 53 optimal weight:    9.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 200 ASN
** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 458 ASN
** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 754 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.079471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.050247 restraints weight = 28847.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.052194 restraints weight = 20393.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.053742 restraints weight = 15912.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3089
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3089 r_free = 0.3089    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3089 r_free = 0.3089    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3089
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.7833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6141  Z= 0.171
  Angle     :  0.615   9.546   8286  Z= 0.322
  Chirality :  0.041   0.164    892
  Planarity :  0.004   0.041   1060
  Dihedral  :  7.135 130.519    814
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.31), residues: 733
  helix:  1.25 (0.27), residues: 362
  sheet: -0.21 (0.50), residues: 98
  loop : -0.24 (0.38), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  22 
 HIS   0.009   0.001   HIS A 552 
 PHE   0.028   0.002   PHE A 639 
 TYR   0.021   0.002   TYR A 263 
 ARG   0.006   0.001   ARG A 309 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.9423 (mp0) cc_final: 0.9198 (mp0)
REVERT: A   22 TRP cc_start: 0.9337 (m100) cc_final: 0.8849 (m100)
REVERT: A   92 ARG cc_start: 0.9620 (tpt170) cc_final: 0.9306 (tpp80)
REVERT: A  139 ILE cc_start: 0.9582 (tt) cc_final: 0.9381 (tt)
REVERT: A  140 PHE cc_start: 0.8843 (m-80) cc_final: 0.8195 (m-80)
REVERT: A  170 THR cc_start: 0.9660 (m) cc_final: 0.9439 (m)
REVERT: A  262 PHE cc_start: 0.9566 (m-80) cc_final: 0.9228 (m-80)
REVERT: A  304 GLU cc_start: 0.9389 (mp0) cc_final: 0.8840 (mp0)
REVERT: A  319 GLU cc_start: 0.8722 (tp30) cc_final: 0.7994 (tp30)
REVERT: A  323 MET cc_start: 0.9301 (mmp) cc_final: 0.9093 (mmm)
REVERT: A  340 PHE cc_start: 0.7182 (p90) cc_final: 0.6639 (p90)
REVERT: A  360 PHE cc_start: 0.9227 (t80) cc_final: 0.8910 (t80)
REVERT: A  460 LYS cc_start: 0.9691 (tptt) cc_final: 0.9375 (tmtt)
REVERT: A  559 TYR cc_start: 0.8246 (m-80) cc_final: 0.7489 (m-80)
REVERT: A  567 LYS cc_start: 0.9699 (ptpt) cc_final: 0.9479 (pttm)
REVERT: A  692 ILE cc_start: 0.9142 (pt) cc_final: 0.8896 (pt)
REVERT: A  701 TRP cc_start: 0.9419 (m-90) cc_final: 0.8562 (m-90)
REVERT: A  714 MET cc_start: 0.6389 (tpp) cc_final: 0.6035 (tpp)
REVERT: A  746 THR cc_start: 0.8253 (m) cc_final: 0.8045 (p)
REVERT: A  750 PHE cc_start: 0.9213 (m-80) cc_final: 0.7883 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.2453
  time to fit residues: 41.7951
Evaluate side-chains
  110 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 56 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 39 optimal weight:    0.5980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 200 ASN
** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 754 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.079387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.050231 restraints weight = 29677.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.052231 restraints weight = 21166.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.053678 restraints weight = 16499.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3092
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3092
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.8008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6141  Z= 0.175
  Angle     :  0.602   6.584   8286  Z= 0.319
  Chirality :  0.041   0.173    892
  Planarity :  0.004   0.040   1060
  Dihedral  :  7.091 130.683    814
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.31), residues: 733
  helix:  1.26 (0.27), residues: 362
  sheet: -0.16 (0.50), residues: 98
  loop : -0.19 (0.38), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  22 
 HIS   0.005   0.001   HIS A 552 
 PHE   0.029   0.002   PHE A 639 
 TYR   0.018   0.002   TYR A 263 
 ARG   0.004   0.001   ARG A 700 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.9415 (mp0) cc_final: 0.9178 (mp0)
REVERT: A   22 TRP cc_start: 0.9362 (m100) cc_final: 0.8869 (m100)
REVERT: A   92 ARG cc_start: 0.9604 (tpt170) cc_final: 0.9296 (tpp80)
REVERT: A  140 PHE cc_start: 0.8867 (m-80) cc_final: 0.8262 (m-80)
REVERT: A  219 ARG cc_start: 0.8561 (mmp80) cc_final: 0.7884 (mmp80)
REVERT: A  262 PHE cc_start: 0.9567 (m-80) cc_final: 0.9230 (m-80)
REVERT: A  304 GLU cc_start: 0.9363 (mp0) cc_final: 0.8916 (mp0)
REVERT: A  308 THR cc_start: 0.9728 (p) cc_final: 0.9430 (p)
REVERT: A  323 MET cc_start: 0.9290 (mmp) cc_final: 0.9023 (mmm)
REVERT: A  340 PHE cc_start: 0.7155 (p90) cc_final: 0.6627 (p90)
REVERT: A  364 MET cc_start: 0.9070 (mmp) cc_final: 0.8814 (mmp)
REVERT: A  436 LEU cc_start: 0.9567 (tp) cc_final: 0.9261 (tp)
REVERT: A  439 TYR cc_start: 0.8392 (p90) cc_final: 0.7854 (p90)
REVERT: A  460 LYS cc_start: 0.9671 (tptt) cc_final: 0.9347 (tptp)
REVERT: A  466 ASN cc_start: 0.9680 (t0) cc_final: 0.9456 (t0)
REVERT: A  467 MET cc_start: 0.9275 (tmm) cc_final: 0.8826 (ppp)
REVERT: A  559 TYR cc_start: 0.8120 (m-80) cc_final: 0.7336 (m-80)
REVERT: A  580 LEU cc_start: 0.9292 (mm) cc_final: 0.8932 (pp)
REVERT: A  588 LEU cc_start: 0.9240 (mt) cc_final: 0.8976 (mt)
REVERT: A  692 ILE cc_start: 0.9197 (pt) cc_final: 0.8977 (pt)
REVERT: A  701 TRP cc_start: 0.9464 (m-90) cc_final: 0.8331 (m-90)
REVERT: A  750 PHE cc_start: 0.9259 (m-80) cc_final: 0.7345 (m-80)
REVERT: A  754 GLN cc_start: 0.6065 (mp10) cc_final: 0.5693 (pp30)
REVERT: A  755 VAL cc_start: 0.8696 (t) cc_final: 0.8065 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.2071
  time to fit residues: 34.1330
Evaluate side-chains
  111 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    0.3980
   chunk 25 optimal weight:    8.9990
   chunk 37 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 29 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   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 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 421 GLN
** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 552 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 = 0.3635 r_free = 0.3635 target = 0.080696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.050745 restraints weight = 29576.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.052755 restraints weight = 21061.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.054188 restraints weight = 16410.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3095
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3095 r_free = 0.3095    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3095 r_free = 0.3095    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3095
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.8150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6141  Z= 0.160
  Angle     :  0.599   6.557   8286  Z= 0.316
  Chirality :  0.041   0.169    892
  Planarity :  0.004   0.040   1060
  Dihedral  :  7.025 129.699    814
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.31), residues: 733
  helix:  1.34 (0.27), residues: 362
  sheet: -0.05 (0.50), residues: 98
  loop : -0.12 (0.39), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  22 
 HIS   0.003   0.001   HIS A 406 
 PHE   0.033   0.002   PHE A 639 
 TYR   0.016   0.002   TYR A 263 
 ARG   0.004   0.001   ARG A 219 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.9429 (mp0) cc_final: 0.9187 (mp0)
REVERT: A   22 TRP cc_start: 0.9378 (m100) cc_final: 0.8900 (m100)
REVERT: A   92 ARG cc_start: 0.9607 (tpt170) cc_final: 0.9297 (tpp80)
REVERT: A  139 ILE cc_start: 0.9569 (tt) cc_final: 0.9348 (tt)
REVERT: A  140 PHE cc_start: 0.8831 (m-80) cc_final: 0.8204 (m-80)
REVERT: A  219 ARG cc_start: 0.8508 (mmp80) cc_final: 0.7773 (mmp80)
REVERT: A  262 PHE cc_start: 0.9574 (m-80) cc_final: 0.9254 (m-80)
REVERT: A  304 GLU cc_start: 0.9335 (mp0) cc_final: 0.8793 (mp0)
REVERT: A  308 THR cc_start: 0.9776 (p) cc_final: 0.9526 (p)
REVERT: A  319 GLU cc_start: 0.8689 (tp30) cc_final: 0.7880 (tp30)
REVERT: A  323 MET cc_start: 0.9276 (mmp) cc_final: 0.9025 (mmm)
REVERT: A  340 PHE cc_start: 0.7197 (p90) cc_final: 0.6652 (p90)
REVERT: A  360 PHE cc_start: 0.9230 (t80) cc_final: 0.8594 (t80)
REVERT: A  364 MET cc_start: 0.9064 (mmp) cc_final: 0.8799 (ptt)
REVERT: A  371 MET cc_start: 0.9486 (tmm) cc_final: 0.9277 (tmm)
REVERT: A  436 LEU cc_start: 0.9568 (tp) cc_final: 0.9300 (tp)
REVERT: A  439 TYR cc_start: 0.8461 (p90) cc_final: 0.7868 (p90)
REVERT: A  460 LYS cc_start: 0.9660 (tptt) cc_final: 0.9361 (tptp)
REVERT: A  466 ASN cc_start: 0.9677 (t0) cc_final: 0.9441 (t0)
REVERT: A  467 MET cc_start: 0.9297 (tmm) cc_final: 0.8827 (ppp)
REVERT: A  559 TYR cc_start: 0.8068 (m-80) cc_final: 0.7701 (m-80)
REVERT: A  580 LEU cc_start: 0.9295 (mm) cc_final: 0.8882 (pp)
REVERT: A  588 LEU cc_start: 0.9225 (mt) cc_final: 0.8803 (mt)
REVERT: A  676 ARG cc_start: 0.9584 (mmm160) cc_final: 0.9175 (mmm160)
REVERT: A  692 ILE cc_start: 0.9206 (pt) cc_final: 0.8988 (pt)
REVERT: A  701 TRP cc_start: 0.9472 (m-90) cc_final: 0.8594 (m-90)
REVERT: A  710 TYR cc_start: 0.7998 (m-80) cc_final: 0.7325 (m-80)
REVERT: A  750 PHE cc_start: 0.9234 (m-80) cc_final: 0.7841 (m-80)
REVERT: A  755 VAL cc_start: 0.8633 (t) cc_final: 0.8276 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.2118
  time to fit residues: 37.3622
Evaluate side-chains
  120 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 47 optimal weight:   10.0000
   chunk 69 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 49 optimal weight:    4.9990
   chunk 33 optimal weight:   10.0000
   chunk 44 optimal weight:    2.9990
   chunk 22 optimal weight:    7.9990
   chunk 3 optimal weight:    8.9990
   chunk 68 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 497 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 = 0.3605 r_free = 0.3605 target = 0.079095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.049537 restraints weight = 30292.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.051465 restraints weight = 21471.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.052821 restraints weight = 16705.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3066
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3066
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.8343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6141  Z= 0.190
  Angle     :  0.609   6.564   8286  Z= 0.322
  Chirality :  0.041   0.171    892
  Planarity :  0.004   0.037   1060
  Dihedral  :  7.122 129.024    814
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.31), residues: 733
  helix:  1.23 (0.27), residues: 362
  sheet: -0.20 (0.49), residues: 99
  loop : -0.14 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 414 
 HIS   0.004   0.001   HIS A 552 
 PHE   0.031   0.002   PHE A 639 
 TYR   0.017   0.002   TYR A 263 
 ARG   0.006   0.001   ARG A 309 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2237.38 seconds
wall clock time: 41 minutes 23.95 seconds (2483.95 seconds total)