Starting phenix.real_space_refine
on Tue Mar 11 14:29:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rbg_19031/03_2025/8rbg_19031.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rbg_19031/03_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_19031/03_2025/8rbg_19031.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rbg_19031/03_2025/8rbg_19031.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rbg_19031/03_2025/8rbg_19031.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rbg_19031/03_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-5624/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: 3.54, per 1000 atoms: 0.59
  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: 1.68
  Conformation dependent library (CDL) restraints added in 943.0 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: 0.67
  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: 1.36

  Time building geometry restraints manager: 1.49 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:             0.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     16.210
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.660
-------------------------------------------------------------------------------
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  : 0.728 
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: 0.2506
  time to fit residues: 69.9682
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  : 0.727 
-------------------------------------------------------------------------------
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 = 0.086423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.054360 restraints weight = 25379.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.056361 restraints weight = 18241.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.058041 restraints weight = 14405.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3190
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    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 = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3187
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
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  : 0.736 
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: 0.8738 (t0) cc_final: 0.7855 (t0)
REVERT: A  262 PHE cc_start: 0.9434 (m-80) cc_final: 0.8613 (m-80)
REVERT: A  304 GLU cc_start: 0.8760 (mp0) cc_final: 0.8365 (mp0)
REVERT: A  326 PHE cc_start: 0.9358 (m-80) cc_final: 0.9052 (m-80)
REVERT: A  360 PHE cc_start: 0.9413 (t80) cc_final: 0.8980 (t80)
REVERT: A  371 MET cc_start: 0.9433 (mtm) cc_final: 0.8995 (mtt)
REVERT: A  387 TYR cc_start: 0.8610 (t80) cc_final: 0.8292 (t80)
REVERT: A  408 TYR cc_start: 0.8710 (t80) cc_final: 0.8162 (t80)
REVERT: A  410 LYS cc_start: 0.8887 (mmtt) cc_final: 0.8653 (mttt)
REVERT: A  438 ILE cc_start: 0.9062 (mm) cc_final: 0.8765 (mm)
REVERT: A  439 TYR cc_start: 0.8886 (p90) cc_final: 0.8450 (p90)
REVERT: A  460 LYS cc_start: 0.9795 (tptt) cc_final: 0.9482 (tptp)
REVERT: A  527 LEU cc_start: 0.9692 (mt) cc_final: 0.9443 (mt)
REVERT: A  557 VAL cc_start: 0.9301 (t) cc_final: 0.8815 (t)
REVERT: A  559 TYR cc_start: 0.8424 (m-80) cc_final: 0.7092 (m-80)
REVERT: A  564 PHE cc_start: 0.9610 (m-80) cc_final: 0.8977 (m-80)
REVERT: A  580 LEU cc_start: 0.9286 (mm) cc_final: 0.8912 (pp)
REVERT: A  648 GLU cc_start: 0.9607 (mt-10) cc_final: 0.9398 (mt-10)
REVERT: A  701 TRP cc_start: 0.9550 (m-90) cc_final: 0.9153 (m-90)
REVERT: A  710 TYR cc_start: 0.8148 (m-80) cc_final: 0.7782 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 169
  average time/residue: 0.2296
  time to fit residues: 48.3890
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  : 0.726 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    6.9990
   chunk 16 optimal weight:   10.0000
   chunk 9 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 72 optimal weight:   20.0000
   chunk 50 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.7586

-------------------------------------------------------------------------------
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 ** 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 = 0.3644 r_free = 0.3644 target = 0.082085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.051769 restraints weight = 26840.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.053739 restraints weight = 19244.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.055225 restraints weight = 15060.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3125
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3125 r_free = 0.3125    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 = 0.3125 r_free = 0.3125    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3125
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.5730

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= 0.207
  Angle     :  0.637   6.759   8286  Z= 0.339
  Chirality :  0.041   0.155    892
  Planarity :  0.005   0.062   1060
  Dihedral  :  7.218 132.737    814
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.64 %
    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:  0.99 (0.31), residues: 733
  helix:  1.52 (0.27), residues: 366
  sheet:  0.26 (0.47), residues: 98
  loop : -0.30 (0.39), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 701 
 HIS   0.007   0.002   HIS A 468 
 PHE   0.026   0.002   PHE A 140 
 TYR   0.020   0.002   TYR A 259 
 ARG   0.008   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
  152 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 0.756 
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: A   92 ARG cc_start: 0.9589 (tpt170) cc_final: 0.9294 (tpp80)
REVERT: A  135 MET cc_start: 0.7663 (mtp) cc_final: 0.7344 (mtp)
REVERT: A  140 PHE cc_start: 0.8705 (m-80) cc_final: 0.7995 (m-80)
REVERT: A  258 ASN cc_start: 0.8501 (t0) cc_final: 0.7628 (t0)
REVERT: A  262 PHE cc_start: 0.9461 (m-80) cc_final: 0.8378 (m-80)
REVERT: A  360 PHE cc_start: 0.9350 (t80) cc_final: 0.8896 (t80)
REVERT: A  387 TYR cc_start: 0.8562 (t80) cc_final: 0.8234 (t80)
REVERT: A  408 TYR cc_start: 0.8725 (t80) cc_final: 0.8207 (t80)
REVERT: A  410 LYS cc_start: 0.8835 (mmtt) cc_final: 0.8471 (mttt)
REVERT: A  438 ILE cc_start: 0.9095 (mm) cc_final: 0.8814 (mm)
REVERT: A  459 GLU cc_start: 0.9456 (mm-30) cc_final: 0.9116 (mm-30)
REVERT: A  460 LYS cc_start: 0.9779 (tptt) cc_final: 0.9499 (tptp)
REVERT: A  527 LEU cc_start: 0.9661 (mt) cc_final: 0.9345 (mt)
REVERT: A  548 PHE cc_start: 0.9335 (p90) cc_final: 0.8896 (p90)
REVERT: A  552 HIS cc_start: 0.8200 (m90) cc_final: 0.7563 (m90)
REVERT: A  559 TYR cc_start: 0.8734 (m-80) cc_final: 0.7705 (m-80)
REVERT: A  648 GLU cc_start: 0.9633 (mt-10) cc_final: 0.9406 (mt-10)
REVERT: A  676 ARG cc_start: 0.9485 (tpt90) cc_final: 0.8824 (mmm160)
REVERT: A  688 GLU cc_start: 0.9289 (mt-10) cc_final: 0.9029 (mt-10)
REVERT: A  750 PHE cc_start: 0.8844 (m-80) cc_final: 0.7367 (m-10)
REVERT: A  755 VAL cc_start: 0.8712 (t) cc_final: 0.8450 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 152
  average time/residue: 0.2143
  time to fit residues: 41.0687
Evaluate side-chains
  115 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 8 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 49 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 68 optimal weight:   30.0000
   chunk 6 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 191 ASN
** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 337 ASN ** 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 458 ASN
A 468 HIS
** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.071839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.043875 restraints weight = 32821.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.045586 restraints weight = 23184.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.046874 restraints weight = 18108.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2929
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2929
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.7195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062   6141  Z= 0.475
  Angle     :  0.913  10.328   8286  Z= 0.480
  Chirality :  0.047   0.170    892
  Planarity :  0.007   0.082   1060
  Dihedral  :  8.325 139.247    814
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 29.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  4.04 %
    Favored  : 95.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.29), residues: 733
  helix:  0.11 (0.25), residues: 359
  sheet: -0.74 (0.45), residues: 94
  loop : -0.81 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.005   TRP A  22 
 HIS   0.012   0.003   HIS A  87 
 PHE   0.030   0.003   PHE A 140 
 TYR   0.034   0.004   TYR A 113 
 ARG   0.010   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
  129 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.679 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 ARG cc_start: 0.9610 (tpt170) cc_final: 0.9295 (tpp80)
REVERT: A  140 PHE cc_start: 0.8967 (m-80) cc_final: 0.8114 (m-80)
REVERT: A  179 TYR cc_start: 0.9506 (t80) cc_final: 0.9131 (t80)
REVERT: A  259 TYR cc_start: 0.9108 (m-80) cc_final: 0.8564 (m-10)
REVERT: A  262 PHE cc_start: 0.9527 (m-80) cc_final: 0.9026 (m-80)
REVERT: A  340 PHE cc_start: 0.6925 (p90) cc_final: 0.6542 (p90)
REVERT: A  360 PHE cc_start: 0.9277 (t80) cc_final: 0.8626 (t80)
REVERT: A  438 ILE cc_start: 0.8886 (mm) cc_final: 0.8579 (mm)
REVERT: A  456 TYR cc_start: 0.9612 (t80) cc_final: 0.9201 (t80)
REVERT: A  459 GLU cc_start: 0.9553 (mm-30) cc_final: 0.9274 (mm-30)
REVERT: A  460 LYS cc_start: 0.9787 (tptt) cc_final: 0.9581 (tptp)
REVERT: A  552 HIS cc_start: 0.8593 (m90) cc_final: 0.8032 (m90)
REVERT: A  559 TYR cc_start: 0.8548 (m-80) cc_final: 0.7877 (m-80)
REVERT: A  664 ASN cc_start: 0.8891 (t0) cc_final: 0.8353 (p0)
REVERT: A  676 ARG cc_start: 0.9676 (mmm160) cc_final: 0.9290 (mmm160)
REVERT: A  688 GLU cc_start: 0.9313 (mt-10) cc_final: 0.9086 (mt-10)
REVERT: A  709 ARG cc_start: 0.9560 (mmp80) cc_final: 0.9297 (ptp-110)
  outliers start: 1
  outliers final: 0
  residues processed: 129
  average time/residue: 0.2092
  time to fit residues: 34.6849
Evaluate side-chains
  97 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 53 optimal weight:   10.0000
   chunk 68 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    0.1980
   chunk 65 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 28 optimal weight:    6.9990
   chunk 47 optimal weight:    4.9990
   chunk 19 optimal weight:    7.9990
   overall best weight:    1.5182

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

Flipped N/Q/H residues before XYZ refinement:
** A  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 290 GLN
** A 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 429 GLN
A 468 HIS
A 637 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.077484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.048171 restraints weight = 29781.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.050103 restraints weight = 20907.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.051574 restraints weight = 16193.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3045
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3045
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.7315

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= 0.204
  Angle     :  0.630   6.697   8286  Z= 0.332
  Chirality :  0.041   0.151    892
  Planarity :  0.005   0.052   1060
  Dihedral  :  7.660 141.013    814
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 16.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  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:  0.09 (0.30), residues: 733
  helix:  0.92 (0.27), residues: 359
  sheet: -0.78 (0.45), residues: 99
  loop : -0.62 (0.36), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  22 
 HIS   0.006   0.001   HIS A 552 
 PHE   0.015   0.002   PHE A 326 
 TYR   0.022   0.002   TYR A 263 
 ARG   0.005   0.001   ARG A 309 

*********************** 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  : 0.737 
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: 0.9311 (m100) cc_final: 0.8903 (m100)
REVERT: A   92 ARG cc_start: 0.9611 (tpt170) cc_final: 0.9125 (mmm160)
REVERT: A  135 MET cc_start: 0.7771 (mtp) cc_final: 0.7535 (mtp)
REVERT: A  140 PHE cc_start: 0.8630 (m-80) cc_final: 0.7969 (m-80)
REVERT: A  219 ARG cc_start: 0.8815 (mmp80) cc_final: 0.8435 (mmp80)
REVERT: A  259 TYR cc_start: 0.9178 (m-80) cc_final: 0.8708 (m-10)
REVERT: A  262 PHE cc_start: 0.9547 (m-80) cc_final: 0.9112 (m-80)
REVERT: A  314 LEU cc_start: 0.9667 (mt) cc_final: 0.9434 (mm)
REVERT: A  340 PHE cc_start: 0.6968 (p90) cc_final: 0.6396 (p90)
REVERT: A  360 PHE cc_start: 0.9104 (t80) cc_final: 0.8774 (t80)
REVERT: A  406 HIS cc_start: 0.9131 (t70) cc_final: 0.8771 (t-90)
REVERT: A  438 ILE cc_start: 0.8767 (mm) cc_final: 0.8359 (mm)
REVERT: A  439 TYR cc_start: 0.8817 (p90) cc_final: 0.8474 (p90)
REVERT: A  456 TYR cc_start: 0.9551 (t80) cc_final: 0.9060 (t80)
REVERT: A  459 GLU cc_start: 0.9479 (mm-30) cc_final: 0.9241 (mm-30)
REVERT: A  460 LYS cc_start: 0.9773 (tptt) cc_final: 0.9466 (tptp)
REVERT: A  580 LEU cc_start: 0.9314 (mm) cc_final: 0.8973 (pp)
REVERT: A  639 PHE cc_start: 0.9182 (t80) cc_final: 0.8752 (t80)
REVERT: A  676 ARG cc_start: 0.9638 (mmm160) cc_final: 0.9194 (mmm160)
REVERT: A  688 GLU cc_start: 0.9268 (mt-10) cc_final: 0.9050 (mt-10)
REVERT: A  701 TRP cc_start: 0.9488 (m-90) cc_final: 0.8952 (m-90)
REVERT: A  714 MET cc_start: 0.7274 (tpp) cc_final: 0.6999 (tpp)
REVERT: A  748 ILE cc_start: 0.9025 (mp) cc_final: 0.7818 (mp)
REVERT: A  750 PHE cc_start: 0.9339 (m-10) cc_final: 0.8399 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.2081
  time to fit residues: 34.6930
Evaluate side-chains
  97 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 66 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 3 optimal weight:   10.0000
   chunk 55 optimal weight:    0.0980
   chunk 58 optimal weight:    4.9990
   chunk 46 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** A  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 310 GLN
** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 354 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 468 HIS
** 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 = 0.3588 r_free = 0.3588 target = 0.077534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.048286 restraints weight = 28949.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.050193 restraints weight = 20851.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.051537 restraints weight = 16355.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3054
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3054
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
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= 0.187
  Angle     :  0.614   6.664   8286  Z= 0.323
  Chirality :  0.041   0.231    892
  Planarity :  0.004   0.049   1060
  Dihedral  :  7.436 135.776    814
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  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:  0.35 (0.30), residues: 733
  helix:  1.13 (0.27), residues: 360
  sheet: -0.69 (0.47), residues: 99
  loop : -0.49 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 523 
 HIS   0.004   0.001   HIS A 286 
 PHE   0.014   0.001   PHE A 360 
 TYR   0.028   0.002   TYR A 113 
 ARG   0.004   0.001   ARG A 309 

*********************** 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
  126 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.722 
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: 0.9393 (mp0) cc_final: 0.9123 (mp0)
REVERT: A   22 TRP cc_start: 0.9304 (m100) cc_final: 0.8818 (m100)
REVERT: A   92 ARG cc_start: 0.9611 (tpt170) cc_final: 0.9299 (tpp80)
REVERT: A  139 ILE cc_start: 0.9576 (tt) cc_final: 0.9374 (tt)
REVERT: A  140 PHE cc_start: 0.8694 (m-80) cc_final: 0.8063 (m-80)
REVERT: A  219 ARG cc_start: 0.8773 (mmp80) cc_final: 0.8378 (mmp80)
REVERT: A  259 TYR cc_start: 0.9095 (m-80) cc_final: 0.8730 (m-10)
REVERT: A  262 PHE cc_start: 0.9577 (m-80) cc_final: 0.9175 (m-80)
REVERT: A  340 PHE cc_start: 0.6997 (p90) cc_final: 0.6418 (p90)
REVERT: A  360 PHE cc_start: 0.9085 (t80) cc_final: 0.8776 (t80)
REVERT: A  406 HIS cc_start: 0.9123 (t70) cc_final: 0.8812 (t-90)
REVERT: A  438 ILE cc_start: 0.8814 (mm) cc_final: 0.8454 (mm)
REVERT: A  456 TYR cc_start: 0.9524 (t80) cc_final: 0.9104 (t80)
REVERT: A  459 GLU cc_start: 0.9538 (mm-30) cc_final: 0.9182 (mm-30)
REVERT: A  460 LYS cc_start: 0.9758 (tptt) cc_final: 0.9463 (tptp)
REVERT: A  517 LYS cc_start: 0.9538 (mmpt) cc_final: 0.9326 (mmtm)
REVERT: A  580 LEU cc_start: 0.9372 (mm) cc_final: 0.9063 (pp)
REVERT: A  639 PHE cc_start: 0.9179 (t80) cc_final: 0.8802 (t80)
REVERT: A  676 ARG cc_start: 0.9628 (mmm160) cc_final: 0.9159 (mmm160)
REVERT: A  692 ILE cc_start: 0.9151 (pt) cc_final: 0.8916 (pt)
REVERT: A  701 TRP cc_start: 0.9441 (m-90) cc_final: 0.8597 (m-90)
REVERT: A  714 MET cc_start: 0.7231 (tpp) cc_final: 0.7010 (tpp)
REVERT: A  750 PHE cc_start: 0.9416 (m-10) cc_final: 0.8806 (m-10)
REVERT: A  755 VAL cc_start: 0.8585 (t) cc_final: 0.8317 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.2100
  time to fit residues: 33.7565
Evaluate side-chains
  105 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 0 optimal weight:    9.9990
   chunk 59 optimal weight:    8.9990
   chunk 29 optimal weight:    0.3980
   chunk 15 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 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**
A 754 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.079686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.049711 restraints weight = 29038.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.051664 restraints weight = 20857.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.053102 restraints weight = 16339.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3096
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    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 = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3096
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.7776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6141  Z= 0.165
  Angle     :  0.590   6.604   8286  Z= 0.309
  Chirality :  0.040   0.199    892
  Planarity :  0.004   0.049   1060
  Dihedral  :  7.185 134.522    814
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  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:  0.58 (0.31), residues: 733
  helix:  1.25 (0.27), residues: 363
  sheet: -0.40 (0.47), residues: 95
  loop : -0.37 (0.37), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  22 
 HIS   0.004   0.001   HIS A 286 
 PHE   0.015   0.001   PHE A 360 
 TYR   0.014   0.002   TYR A 263 
 ARG   0.006   0.000   ARG A 309 

*********************** 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
  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: A   20 GLU cc_start: 0.9408 (mp0) cc_final: 0.9115 (mp0)
REVERT: A   22 TRP cc_start: 0.9370 (m100) cc_final: 0.8862 (m100)
REVERT: A   92 ARG cc_start: 0.9618 (tpt170) cc_final: 0.9304 (tpp80)
REVERT: A  140 PHE cc_start: 0.8639 (m-80) cc_final: 0.8031 (m-80)
REVERT: A  219 ARG cc_start: 0.8824 (mmp80) cc_final: 0.8434 (mmp80)
REVERT: A  259 TYR cc_start: 0.9099 (m-80) cc_final: 0.8668 (m-10)
REVERT: A  262 PHE cc_start: 0.9555 (m-80) cc_final: 0.9136 (m-80)
REVERT: A  304 GLU cc_start: 0.9410 (mp0) cc_final: 0.8858 (mp0)
REVERT: A  323 MET cc_start: 0.9363 (mmp) cc_final: 0.9132 (mmm)
REVERT: A  340 PHE cc_start: 0.7066 (p90) cc_final: 0.6501 (p90)
REVERT: A  360 PHE cc_start: 0.9035 (t80) cc_final: 0.8777 (t80)
REVERT: A  406 HIS cc_start: 0.9072 (t70) cc_final: 0.8862 (t-90)
REVERT: A  436 LEU cc_start: 0.9513 (tp) cc_final: 0.9295 (tp)
REVERT: A  438 ILE cc_start: 0.8554 (mm) cc_final: 0.8239 (mm)
REVERT: A  439 TYR cc_start: 0.8896 (p90) cc_final: 0.8647 (p90)
REVERT: A  456 TYR cc_start: 0.9507 (t80) cc_final: 0.9072 (t80)
REVERT: A  459 GLU cc_start: 0.9467 (mm-30) cc_final: 0.9112 (mm-30)
REVERT: A  460 LYS cc_start: 0.9745 (tptt) cc_final: 0.9480 (tmtt)
REVERT: A  517 LYS cc_start: 0.9488 (mmpt) cc_final: 0.9279 (mmtm)
REVERT: A  559 TYR cc_start: 0.7971 (m-80) cc_final: 0.7345 (m-80)
REVERT: A  580 LEU cc_start: 0.9378 (mm) cc_final: 0.9095 (pp)
REVERT: A  639 PHE cc_start: 0.9227 (t80) cc_final: 0.8858 (t80)
REVERT: A  676 ARG cc_start: 0.9606 (mmm160) cc_final: 0.8977 (mmm160)
REVERT: A  692 ILE cc_start: 0.9188 (pt) cc_final: 0.8966 (pt)
REVERT: A  701 TRP cc_start: 0.9482 (m-90) cc_final: 0.8952 (m-90)
REVERT: A  750 PHE cc_start: 0.9482 (m-10) cc_final: 0.9171 (m-10)
REVERT: A  755 VAL cc_start: 0.8566 (t) cc_final: 0.8281 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.2048
  time to fit residues: 34.4455
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  : 0.731 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 53 optimal weight:    7.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 337 ASN ** 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 462 GLN
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 = 0.079512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.049401 restraints weight = 29096.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.051244 restraints weight = 21009.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.052768 restraints weight = 16645.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3077
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3077 r_free = 0.3077    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 = 0.3077 r_free = 0.3077    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3077
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.7995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6141  Z= 0.163
  Angle     :  0.596   6.595   8286  Z= 0.310
  Chirality :  0.040   0.186    892
  Planarity :  0.004   0.042   1060
  Dihedral  :  7.084 131.300    814
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  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:  0.70 (0.31), residues: 733
  helix:  1.29 (0.28), residues: 363
  sheet: -0.25 (0.49), residues: 95
  loop : -0.28 (0.37), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  22 
 HIS   0.004   0.001   HIS A 286 
 PHE   0.015   0.001   PHE A 360 
 TYR   0.012   0.001   TYR A 263 
 ARG   0.003   0.000   ARG A  90 

*********************** 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
  131 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.9404 (mp0) cc_final: 0.9091 (mp0)
REVERT: A   22 TRP cc_start: 0.9379 (m100) cc_final: 0.8932 (m100)
REVERT: A   92 ARG cc_start: 0.9625 (tpt170) cc_final: 0.9334 (tpp80)
REVERT: A  140 PHE cc_start: 0.8745 (m-80) cc_final: 0.8130 (m-80)
REVERT: A  219 ARG cc_start: 0.8758 (mmp80) cc_final: 0.8351 (mmp80)
REVERT: A  259 TYR cc_start: 0.9109 (m-80) cc_final: 0.8669 (m-10)
REVERT: A  262 PHE cc_start: 0.9545 (m-80) cc_final: 0.9133 (m-80)
REVERT: A  304 GLU cc_start: 0.9433 (mp0) cc_final: 0.8885 (mp0)
REVERT: A  323 MET cc_start: 0.9270 (mmp) cc_final: 0.9036 (mmm)
REVERT: A  340 PHE cc_start: 0.7024 (p90) cc_final: 0.6527 (p90)
REVERT: A  360 PHE cc_start: 0.9024 (t80) cc_final: 0.8764 (t80)
REVERT: A  436 LEU cc_start: 0.9480 (tp) cc_final: 0.9249 (tp)
REVERT: A  438 ILE cc_start: 0.8567 (mm) cc_final: 0.8284 (mm)
REVERT: A  439 TYR cc_start: 0.8814 (p90) cc_final: 0.8563 (p90)
REVERT: A  456 TYR cc_start: 0.9438 (t80) cc_final: 0.9123 (t80)
REVERT: A  459 GLU cc_start: 0.9480 (mm-30) cc_final: 0.9110 (mm-30)
REVERT: A  460 LYS cc_start: 0.9719 (tptt) cc_final: 0.9409 (tptp)
REVERT: A  467 MET cc_start: 0.9304 (tmm) cc_final: 0.9080 (tmm)
REVERT: A  559 TYR cc_start: 0.8124 (m-80) cc_final: 0.7690 (m-80)
REVERT: A  580 LEU cc_start: 0.9387 (mm) cc_final: 0.9114 (pp)
REVERT: A  639 PHE cc_start: 0.9226 (t80) cc_final: 0.8885 (t80)
REVERT: A  692 ILE cc_start: 0.9200 (pt) cc_final: 0.8973 (pt)
REVERT: A  701 TRP cc_start: 0.9499 (m-90) cc_final: 0.8859 (m-90)
REVERT: A  714 MET cc_start: 0.6304 (tpp) cc_final: 0.6070 (tpp)
REVERT: A  750 PHE cc_start: 0.9512 (m-10) cc_final: 0.9133 (m-10)
REVERT: A  755 VAL cc_start: 0.8537 (t) cc_final: 0.8186 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.1898
  time to fit residues: 32.4667
Evaluate side-chains
  104 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 52 optimal weight:    8.9990
   chunk 66 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 3 optimal weight:    9.9990
   chunk 39 optimal weight:    0.1980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 200 ASN
** 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 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 GLN
A 497 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.079873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.050157 restraints weight = 28908.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.052069 restraints weight = 20595.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.053548 restraints weight = 16169.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3098
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3098 r_free = 0.3098    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 = 0.3098 r_free = 0.3098    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3098
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.8152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6141  Z= 0.158
  Angle     :  0.600   6.572   8286  Z= 0.310
  Chirality :  0.040   0.179    892
  Planarity :  0.004   0.040   1060
  Dihedral  :  6.979 129.497    814
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  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:  0.87 (0.31), residues: 733
  helix:  1.44 (0.28), residues: 363
  sheet: -0.09 (0.50), residues: 95
  loop : -0.23 (0.37), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 414 
 HIS   0.004   0.001   HIS A 418 
 PHE   0.015   0.001   PHE A 360 
 TYR   0.016   0.001   TYR A 710 
 ARG   0.006   0.000   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
  127 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.9389 (mp0) cc_final: 0.9069 (mp0)
REVERT: A   22 TRP cc_start: 0.9385 (m100) cc_final: 0.8988 (m100)
REVERT: A   92 ARG cc_start: 0.9613 (tpt170) cc_final: 0.9317 (tpp80)
REVERT: A  139 ILE cc_start: 0.9584 (tt) cc_final: 0.9378 (tt)
REVERT: A  140 PHE cc_start: 0.8779 (m-80) cc_final: 0.8113 (m-80)
REVERT: A  219 ARG cc_start: 0.8756 (mmp80) cc_final: 0.8382 (mmp80)
REVERT: A  259 TYR cc_start: 0.9077 (m-80) cc_final: 0.8635 (m-10)
REVERT: A  262 PHE cc_start: 0.9537 (m-80) cc_final: 0.9143 (m-80)
REVERT: A  304 GLU cc_start: 0.9393 (mp0) cc_final: 0.8970 (mp0)
REVERT: A  340 PHE cc_start: 0.7075 (p90) cc_final: 0.6529 (p90)
REVERT: A  436 LEU cc_start: 0.9485 (tp) cc_final: 0.9222 (tp)
REVERT: A  438 ILE cc_start: 0.8649 (mm) cc_final: 0.8295 (mm)
REVERT: A  456 TYR cc_start: 0.9431 (t80) cc_final: 0.9053 (t80)
REVERT: A  459 GLU cc_start: 0.9497 (mm-30) cc_final: 0.9201 (mm-30)
REVERT: A  460 LYS cc_start: 0.9722 (tptt) cc_final: 0.9446 (tmtt)
REVERT: A  580 LEU cc_start: 0.9395 (mm) cc_final: 0.9167 (pp)
REVERT: A  639 PHE cc_start: 0.9215 (t80) cc_final: 0.8904 (t80)
REVERT: A  676 ARG cc_start: 0.9588 (mmm160) cc_final: 0.9020 (mmm160)
REVERT: A  692 ILE cc_start: 0.9208 (pt) cc_final: 0.8983 (pt)
REVERT: A  701 TRP cc_start: 0.9534 (m-90) cc_final: 0.8707 (m-90)
REVERT: A  714 MET cc_start: 0.5946 (tpp) cc_final: 0.5687 (tpp)
REVERT: A  750 PHE cc_start: 0.9488 (m-10) cc_final: 0.8994 (m-10)
REVERT: A  755 VAL cc_start: 0.8460 (t) cc_final: 0.8194 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1764
  time to fit residues: 29.6481
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  : 0.734 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0030
   chunk 9 optimal weight:    3.9990
   chunk 55 optimal weight:    7.9990
   chunk 29 optimal weight:    5.9990
   chunk 13 optimal weight:    9.9990
   chunk 32 optimal weight:    8.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    1.2794

-------------------------------------------------------------------------------
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 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.079149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.049508 restraints weight = 29671.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.051426 restraints weight = 21210.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.052891 restraints weight = 16645.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3087
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3087 r_free = 0.3087    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3087 r_free = 0.3087    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3087
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.8293

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= 0.182
  Angle     :  0.616   6.653   8286  Z= 0.319
  Chirality :  0.040   0.169    892
  Planarity :  0.004   0.037   1060
  Dihedral  :  7.051 128.063    814
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  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:  0.87 (0.31), residues: 733
  helix:  1.44 (0.28), residues: 363
  sheet: -0.20 (0.49), residues: 95
  loop : -0.18 (0.38), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP A 414 
 HIS   0.004   0.001   HIS A 418 
 PHE   0.048   0.002   PHE A 360 
 TYR   0.014   0.002   TYR A 263 
 ARG   0.006   0.001   ARG A 700 

********************** 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
  126 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.9386 (mp0) cc_final: 0.9060 (mp0)
REVERT: A   22 TRP cc_start: 0.9408 (m100) cc_final: 0.9096 (m100)
REVERT: A   92 ARG cc_start: 0.9624 (tpt170) cc_final: 0.9314 (tpp80)
REVERT: A  139 ILE cc_start: 0.9588 (tt) cc_final: 0.9376 (tt)
REVERT: A  140 PHE cc_start: 0.8853 (m-80) cc_final: 0.8162 (m-80)
REVERT: A  259 TYR cc_start: 0.8952 (m-80) cc_final: 0.8573 (m-10)
REVERT: A  262 PHE cc_start: 0.9547 (m-80) cc_final: 0.9161 (m-80)
REVERT: A  304 GLU cc_start: 0.9411 (mp0) cc_final: 0.8996 (mp0)
REVERT: A  340 PHE cc_start: 0.7050 (p90) cc_final: 0.6517 (p90)
REVERT: A  360 PHE cc_start: 0.9127 (t80) cc_final: 0.8923 (t80)
REVERT: A  436 LEU cc_start: 0.9482 (tp) cc_final: 0.9210 (tp)
REVERT: A  438 ILE cc_start: 0.8534 (mm) cc_final: 0.8189 (mm)
REVERT: A  439 TYR cc_start: 0.8698 (p90) cc_final: 0.8444 (p90)
REVERT: A  456 TYR cc_start: 0.9445 (t80) cc_final: 0.9072 (t80)
REVERT: A  459 GLU cc_start: 0.9529 (mm-30) cc_final: 0.9214 (mm-30)
REVERT: A  460 LYS cc_start: 0.9728 (tptt) cc_final: 0.9439 (tptp)
REVERT: A  466 ASN cc_start: 0.9685 (t0) cc_final: 0.9464 (t0)
REVERT: A  467 MET cc_start: 0.9260 (tmm) cc_final: 0.8820 (ppp)
REVERT: A  548 PHE cc_start: 0.8985 (p90) cc_final: 0.8660 (p90)
REVERT: A  639 PHE cc_start: 0.9218 (t80) cc_final: 0.8917 (t80)
REVERT: A  676 ARG cc_start: 0.9611 (mmm160) cc_final: 0.9195 (mmm160)
REVERT: A  692 ILE cc_start: 0.9215 (pt) cc_final: 0.8997 (pt)
REVERT: A  700 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7799 (ttp80)
REVERT: A  701 TRP cc_start: 0.9267 (m-90) cc_final: 0.8771 (m-90)
REVERT: A  714 MET cc_start: 0.5811 (tpp) cc_final: 0.5311 (tpp)
REVERT: A  750 PHE cc_start: 0.9492 (m-10) cc_final: 0.8511 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1988
  time to fit residues: 33.1008
Evaluate side-chains
  105 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 47 optimal weight:    9.9990
   chunk 69 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 33 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.5990

-------------------------------------------------------------------------------
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 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.078196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.048391 restraints weight = 30633.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.050374 restraints weight = 21468.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.051823 restraints weight = 16686.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3053
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3053 r_free = 0.3053    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3053 r_free = 0.3053    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3053
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.8466

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= 0.196
  Angle     :  0.625   6.732   8286  Z= 0.323
  Chirality :  0.040   0.160    892
  Planarity :  0.004   0.035   1060
  Dihedral  :  7.094 128.697    814
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 14.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  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:  0.81 (0.31), residues: 733
  helix:  1.40 (0.28), residues: 364
  sheet: -0.38 (0.49), residues: 95
  loop : -0.17 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP A  22 
 HIS   0.004   0.001   HIS A 418 
 PHE   0.045   0.002   PHE A 360 
 TYR   0.015   0.002   TYR A 263 
 ARG   0.006   0.001   ARG A 219 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2284.14 seconds
wall clock time: 40 minutes 44.18 seconds (2444.18 seconds total)