Starting phenix.real_space_refine
on Fri Oct 10 13:27:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rbg_19031/10_2025/8rbg_19031.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rbg_19031/10_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rbg_19031/10_2025/8rbg_19031.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rbg_19031/10_2025/8rbg_19031.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rbg_19031/10_2025/8rbg_19031.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rbg_19031/10_2025/8rbg_19031.map"
  }
  resolution = 4.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.67, per 1000 atoms: 0.28
  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: 0.58
  Conformation dependent library (CDL) restraints added in 362.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.15
  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: 0.70

  Time building geometry restraints manager: 0.71 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:             1.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.390
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.810
-------------------------------------------------------------------------------
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= 0.742
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.019   0.002   ARG A 676 
 TYR   0.146   0.029   TYR A 232 
 PHE   0.096   0.017   PHE A 666 
 TRP   0.072   0.022   TRP A 484 
 HIS   0.014   0.004   HIS A 644 

Details of bonding type rmsd
  covalent geometry    : bond        0.01274 ( 6141)
  covalent geometry    : angle       1.92248 ( 8286)
  hydrogen bonds       : bond        0.17568 (  326)
  hydrogen bonds       : angle       6.91159 (  915)

*********************** 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  : 0.237 
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: A  140 PHE cc_start: 0.7495 (m-10) cc_final: 0.7284 (m-80)
REVERT: A  169 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7507 (pttm)
REVERT: A  180 PHE cc_start: 0.7791 (m-80) cc_final: 0.7581 (m-80)
REVERT: A  216 ASN cc_start: 0.8230 (t0) cc_final: 0.7724 (t0)
REVERT: A  220 PHE cc_start: 0.8255 (p90) cc_final: 0.7882 (p90)
REVERT: A  258 ASN cc_start: 0.7492 (t0) cc_final: 0.7047 (t0)
REVERT: A  262 PHE cc_start: 0.8543 (m-80) cc_final: 0.8005 (m-80)
REVERT: A  296 ILE cc_start: 0.7732 (mt) cc_final: 0.7371 (mm)
REVERT: A  299 VAL cc_start: 0.6230 (t) cc_final: 0.5965 (t)
REVERT: A  416 VAL cc_start: 0.8949 (m) cc_final: 0.8728 (m)
REVERT: A  420 ASN cc_start: 0.8556 (m110) cc_final: 0.8070 (m110)
REVERT: A  439 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.7825 (p90)
REVERT: A  509 LEU cc_start: 0.8934 (tp) cc_final: 0.7982 (tp)
REVERT: A  552 HIS cc_start: 0.7681 (m-70) cc_final: 0.7467 (m90)
REVERT: A  559 TYR cc_start: 0.7804 (m-80) cc_final: 0.7112 (m-80)
  outliers start: 4
  outliers final: 2
  residues processed: 230
  average time/residue: 0.1006
  time to fit residues: 28.3225
Evaluate side-chains
  142 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 138
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
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 420 ASN
** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 429 GLN
A 531 HIS
A 576 GLN
A 637 HIS
A 644 HIS
** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.086791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.054646 restraints weight = 25524.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.056776 restraints weight = 18261.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.058454 restraints weight = 14266.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.059699 restraints weight = 11764.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.060493 restraints weight = 10188.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3242
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3239 r_free = 0.3239    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3239
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
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   0.041   6141  Z= 0.149
  Angle     :  0.675   7.335   8286  Z= 0.363
  Chirality :  0.042   0.193    892
  Planarity :  0.005   0.080   1060
  Dihedral  :  7.286 128.796    814
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.86 %
    Favored  : 97.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.31), residues: 733
  helix:  1.69 (0.27), residues: 365
  sheet: -0.01 (0.46), residues: 104
  loop : -0.17 (0.40), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 327 
 TYR   0.029   0.003   TYR A 368 
 PHE   0.039   0.002   PHE A 360 
 TRP   0.024   0.003   TRP A 523 
 HIS   0.009   0.002   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6141)
  covalent geometry    : angle       0.67459 ( 8286)
  hydrogen bonds       : bond        0.04389 (  326)
  hydrogen bonds       : angle       5.05305 (  915)

*********************** 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
  170 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 169
  time to evaluate  : 0.279 
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   22 TRP cc_start: 0.8892 (m100) cc_final: 0.8654 (m100)
REVERT: A  135 MET cc_start: 0.7581 (mtp) cc_final: 0.7349 (mtp)
REVERT: A  258 ASN cc_start: 0.8802 (t0) cc_final: 0.8183 (t0)
REVERT: A  262 PHE cc_start: 0.9420 (m-80) cc_final: 0.8699 (m-80)
REVERT: A  319 GLU cc_start: 0.8589 (tp30) cc_final: 0.7663 (tp30)
REVERT: A  323 MET cc_start: 0.9374 (mmp) cc_final: 0.9053 (mmp)
REVERT: A  326 PHE cc_start: 0.9333 (m-80) cc_final: 0.9051 (m-80)
REVERT: A  371 MET cc_start: 0.9443 (mtm) cc_final: 0.8927 (mtm)
REVERT: A  387 TYR cc_start: 0.8694 (t80) cc_final: 0.8491 (t80)
REVERT: A  408 TYR cc_start: 0.8693 (t80) cc_final: 0.8350 (t80)
REVERT: A  438 ILE cc_start: 0.9010 (mm) cc_final: 0.8714 (mm)
REVERT: A  439 TYR cc_start: 0.8798 (p90) cc_final: 0.8374 (p90)
REVERT: A  464 GLN cc_start: 0.9460 (tm-30) cc_final: 0.9137 (tm-30)
REVERT: A  527 LEU cc_start: 0.9693 (mt) cc_final: 0.9400 (mt)
REVERT: A  557 VAL cc_start: 0.9270 (t) cc_final: 0.8763 (t)
REVERT: A  559 TYR cc_start: 0.8415 (m-80) cc_final: 0.7026 (m-80)
REVERT: A  564 PHE cc_start: 0.9632 (m-80) cc_final: 0.9059 (m-80)
REVERT: A  580 LEU cc_start: 0.9274 (mm) cc_final: 0.8872 (pp)
REVERT: A  648 GLU cc_start: 0.9622 (mt-10) cc_final: 0.9378 (mt-10)
REVERT: A  700 ARG cc_start: 0.8532 (ttp80) cc_final: 0.8211 (ttp80)
REVERT: A  750 PHE cc_start: 0.8842 (m-80) cc_final: 0.8400 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 170
  average time/residue: 0.0923
  time to fit residues: 19.8861
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  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 54 optimal weight:    7.9990
   chunk 44 optimal weight:    0.3980
   chunk 39 optimal weight:    7.9990
   chunk 18 optimal weight:    0.0050
   chunk 37 optimal weight:    0.6980
   chunk 63 optimal weight:    5.9990
   chunk 33 optimal weight:    0.5980
   chunk 30 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 25 optimal weight:    8.9990
   overall best weight:    1.1396

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
A 264 GLN
** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 463 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.083773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.053404 restraints weight = 26881.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.055430 restraints weight = 19198.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.056976 restraints weight = 15001.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.058139 restraints weight = 12477.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.059092 restraints weight = 10841.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3219
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3218
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.5727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6141  Z= 0.133
  Angle     :  0.624   6.627   8286  Z= 0.331
  Chirality :  0.042   0.175    892
  Planarity :  0.005   0.065   1060
  Dihedral  :  7.096 130.524    814
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.17 %
    Favored  : 97.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.31), residues: 733
  helix:  1.58 (0.27), residues: 366
  sheet:  0.08 (0.47), residues: 104
  loop : -0.26 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  92 
 TYR   0.020   0.002   TYR A 259 
 PHE   0.025   0.002   PHE A 360 
 TRP   0.020   0.002   TRP A 701 
 HIS   0.009   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6141)
  covalent geometry    : angle       0.62387 ( 8286)
  hydrogen bonds       : bond        0.03976 (  326)
  hydrogen bonds       : angle       4.95135 (  915)

*********************** 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  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 ARG cc_start: 0.9610 (tpt170) cc_final: 0.9119 (tpp-160)
REVERT: A  140 PHE cc_start: 0.8987 (m-80) cc_final: 0.8523 (m-80)
REVERT: A  258 ASN cc_start: 0.8468 (t0) cc_final: 0.7545 (t0)
REVERT: A  262 PHE cc_start: 0.9416 (m-80) cc_final: 0.8529 (m-80)
REVERT: A  319 GLU cc_start: 0.8725 (tp30) cc_final: 0.8049 (tp30)
REVERT: A  323 MET cc_start: 0.9414 (mmp) cc_final: 0.9139 (mmp)
REVERT: A  326 PHE cc_start: 0.9304 (m-80) cc_final: 0.8630 (m-80)
REVERT: A  360 PHE cc_start: 0.9325 (t80) cc_final: 0.8714 (t80)
REVERT: A  408 TYR cc_start: 0.8768 (t80) cc_final: 0.8410 (t80)
REVERT: A  438 ILE cc_start: 0.9149 (mm) cc_final: 0.8850 (mm)
REVERT: A  460 LYS cc_start: 0.9735 (tppp) cc_final: 0.9508 (tptp)
REVERT: A  527 LEU cc_start: 0.9640 (mt) cc_final: 0.9345 (mt)
REVERT: A  557 VAL cc_start: 0.9295 (t) cc_final: 0.8975 (t)
REVERT: A  559 TYR cc_start: 0.8778 (m-80) cc_final: 0.8147 (m-80)
REVERT: A  564 PHE cc_start: 0.9664 (m-80) cc_final: 0.9116 (m-80)
REVERT: A  580 LEU cc_start: 0.9290 (mm) cc_final: 0.8804 (pp)
REVERT: A  676 ARG cc_start: 0.9429 (tpt90) cc_final: 0.9028 (mmm160)
REVERT: A  688 GLU cc_start: 0.9278 (mt-10) cc_final: 0.9001 (mt-10)
REVERT: A  701 TRP cc_start: 0.9385 (m-90) cc_final: 0.8810 (m-90)
REVERT: A  714 MET cc_start: 0.7479 (tpp) cc_final: 0.6924 (tpp)
REVERT: A  750 PHE cc_start: 0.8913 (m-80) cc_final: 0.7377 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 151
  average time/residue: 0.0882
  time to fit residues: 16.9044
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  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 61 optimal weight:    0.0020
   chunk 71 optimal weight:    3.9990
   chunk 39 optimal weight:   10.0000
   chunk 62 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 54 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9980
   chunk 3 optimal weight:   10.0000
   chunk 52 optimal weight:    6.9990
   chunk 18 optimal weight:    9.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    1.3992

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.082794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.052623 restraints weight = 28090.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.054681 restraints weight = 19806.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.056203 restraints weight = 15358.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.057285 restraints weight = 12713.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.058217 restraints weight = 11076.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3168
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3168
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.6346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6141  Z= 0.136
  Angle     :  0.616   7.218   8286  Z= 0.322
  Chirality :  0.040   0.160    892
  Planarity :  0.004   0.056   1060
  Dihedral  :  7.102 133.554    814
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.17 %
    Favored  : 97.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.31), residues: 733
  helix:  1.41 (0.27), residues: 366
  sheet:  0.20 (0.47), residues: 96
  loop : -0.36 (0.38), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 278 
 TYR   0.018   0.002   TYR A 259 
 PHE   0.019   0.002   PHE A 360 
 TRP   0.025   0.002   TRP A 523 
 HIS   0.007   0.001   HIS A 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 6141)
  covalent geometry    : angle       0.61641 ( 8286)
  hydrogen bonds       : bond        0.03677 (  326)
  hydrogen bonds       : angle       5.00968 (  915)

*********************** 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
  143 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 ARG cc_start: 0.9589 (tpt170) cc_final: 0.9103 (mmm160)
REVERT: A  140 PHE cc_start: 0.8956 (m-80) cc_final: 0.8206 (m-80)
REVERT: A  220 PHE cc_start: 0.9127 (p90) cc_final: 0.8916 (p90)
REVERT: A  239 MET cc_start: 0.8729 (tmm) cc_final: 0.8501 (tmm)
REVERT: A  258 ASN cc_start: 0.8444 (t0) cc_final: 0.7621 (t0)
REVERT: A  262 PHE cc_start: 0.9454 (m-80) cc_final: 0.8120 (m-80)
REVERT: A  304 GLU cc_start: 0.8954 (mp0) cc_final: 0.8433 (mp0)
REVERT: A  319 GLU cc_start: 0.8948 (tp30) cc_final: 0.8096 (tp30)
REVERT: A  387 TYR cc_start: 0.8535 (t80) cc_final: 0.8309 (t80)
REVERT: A  408 TYR cc_start: 0.8861 (t80) cc_final: 0.8530 (t80)
REVERT: A  438 ILE cc_start: 0.9080 (mm) cc_final: 0.8846 (mm)
REVERT: A  460 LYS cc_start: 0.9729 (tppp) cc_final: 0.9475 (tptp)
REVERT: A  548 PHE cc_start: 0.9342 (p90) cc_final: 0.8835 (p90)
REVERT: A  559 TYR cc_start: 0.8608 (m-80) cc_final: 0.7923 (m-80)
REVERT: A  564 PHE cc_start: 0.9622 (m-80) cc_final: 0.8984 (m-80)
REVERT: A  580 LEU cc_start: 0.9179 (mm) cc_final: 0.8869 (pp)
REVERT: A  588 LEU cc_start: 0.9061 (mt) cc_final: 0.8701 (mt)
REVERT: A  676 ARG cc_start: 0.9439 (tpt90) cc_final: 0.8821 (mmm160)
REVERT: A  701 TRP cc_start: 0.9466 (m-90) cc_final: 0.8963 (m-90)
REVERT: A  709 ARG cc_start: 0.9444 (mmp80) cc_final: 0.9220 (mmp80)
REVERT: A  750 PHE cc_start: 0.8971 (m-80) cc_final: 0.7430 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 142
  average time/residue: 0.0745
  time to fit residues: 13.7346
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  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 59 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0870
   chunk 58 optimal weight:    1.9990
   chunk 46 optimal weight:    7.9990
   chunk 4 optimal weight:   10.0000
   chunk 67 optimal weight:    8.9990
   chunk 24 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.9562

-------------------------------------------------------------------------------
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 421 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.081842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.051554 restraints weight = 28577.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.053482 restraints weight = 20551.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.054985 restraints weight = 16197.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.056042 restraints weight = 13511.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.056859 restraints weight = 11807.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3168
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3168
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.6746

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= 0.121
  Angle     :  0.598   7.077   8286  Z= 0.313
  Chirality :  0.040   0.158    892
  Planarity :  0.004   0.053   1060
  Dihedral  :  6.982 134.889    814
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.31), residues: 733
  helix:  1.39 (0.28), residues: 360
  sheet:  0.11 (0.48), residues: 96
  loop : -0.27 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 309 
 TYR   0.013   0.001   TYR A 259 
 PHE   0.021   0.002   PHE A 326 
 TRP   0.010   0.001   TRP A  22 
 HIS   0.005   0.001   HIS A 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 6141)
  covalent geometry    : angle       0.59807 ( 8286)
  hydrogen bonds       : bond        0.03532 (  326)
  hydrogen bonds       : angle       4.87907 (  915)

*********************** 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
  137 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.9391 (mp0) cc_final: 0.9112 (mp0)
REVERT: A   92 ARG cc_start: 0.9618 (tpt170) cc_final: 0.9105 (mmm160)
REVERT: A  135 MET cc_start: 0.7716 (mtp) cc_final: 0.7338 (mpp)
REVERT: A  140 PHE cc_start: 0.8938 (m-80) cc_final: 0.8259 (m-80)
REVERT: A  258 ASN cc_start: 0.8423 (t0) cc_final: 0.7710 (t0)
REVERT: A  262 PHE cc_start: 0.9472 (m-80) cc_final: 0.8261 (m-80)
REVERT: A  304 GLU cc_start: 0.9086 (mp0) cc_final: 0.8787 (mp0)
REVERT: A  319 GLU cc_start: 0.8902 (tp30) cc_final: 0.8125 (tp30)
REVERT: A  326 PHE cc_start: 0.8872 (m-80) cc_final: 0.8537 (m-80)
REVERT: A  360 PHE cc_start: 0.9099 (t80) cc_final: 0.8825 (t80)
REVERT: A  387 TYR cc_start: 0.8490 (t80) cc_final: 0.8276 (t80)
REVERT: A  408 TYR cc_start: 0.8869 (t80) cc_final: 0.8561 (t80)
REVERT: A  414 TRP cc_start: 0.9148 (t60) cc_final: 0.8936 (t60)
REVERT: A  438 ILE cc_start: 0.9198 (mm) cc_final: 0.8889 (mm)
REVERT: A  439 TYR cc_start: 0.8875 (p90) cc_final: 0.8644 (p90)
REVERT: A  460 LYS cc_start: 0.9736 (tppp) cc_final: 0.9489 (tptp)
REVERT: A  527 LEU cc_start: 0.9691 (mt) cc_final: 0.9407 (mt)
REVERT: A  559 TYR cc_start: 0.8548 (m-80) cc_final: 0.8125 (m-80)
REVERT: A  564 PHE cc_start: 0.9624 (m-80) cc_final: 0.8988 (m-80)
REVERT: A  580 LEU cc_start: 0.9189 (mm) cc_final: 0.8768 (pp)
REVERT: A  588 LEU cc_start: 0.9147 (mt) cc_final: 0.8778 (mt)
REVERT: A  676 ARG cc_start: 0.9563 (mmm160) cc_final: 0.9271 (mmm160)
REVERT: A  688 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8877 (tt0)
REVERT: A  701 TRP cc_start: 0.9557 (m-90) cc_final: 0.9006 (m-90)
REVERT: A  750 PHE cc_start: 0.9146 (m-80) cc_final: 0.7548 (m-10)
REVERT: A  755 VAL cc_start: 0.8723 (t) cc_final: 0.8409 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0790
  time to fit residues: 14.2059
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  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 68 optimal weight:    7.9990
   chunk 65 optimal weight:    4.9990
   chunk 55 optimal weight:    6.9990
   chunk 45 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 10 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0770
   chunk 7 optimal weight:    6.9990
   overall best weight:    1.4540

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

Flipped N/Q/H residues before XYZ refinement:
** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 429 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 = 0.3626 r_free = 0.3626 target = 0.080537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.050618 restraints weight = 28663.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.052444 restraints weight = 20936.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.053818 restraints weight = 16624.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.054876 restraints weight = 13972.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.055757 restraints weight = 12248.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3139
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3139 r_free = 0.3139    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3139 r_free = 0.3139    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3139
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.7100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6141  Z= 0.129
  Angle     :  0.611   6.824   8286  Z= 0.317
  Chirality :  0.040   0.152    892
  Planarity :  0.004   0.051   1060
  Dihedral  :  7.033 131.716    814
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.31), residues: 733
  helix:  1.28 (0.28), residues: 360
  sheet: -0.27 (0.46), residues: 102
  loop : -0.16 (0.38), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 309 
 TYR   0.018   0.002   TYR A 703 
 PHE   0.019   0.002   PHE A 360 
 TRP   0.021   0.002   TRP A 523 
 HIS   0.004   0.001   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6141)
  covalent geometry    : angle       0.61081 ( 8286)
  hydrogen bonds       : bond        0.03431 (  326)
  hydrogen bonds       : angle       5.00323 (  915)

*********************** 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
  131 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.9393 (mp0) cc_final: 0.9099 (mp0)
REVERT: A   92 ARG cc_start: 0.9616 (tpt170) cc_final: 0.9119 (mmm160)
REVERT: A  135 MET cc_start: 0.7677 (mtp) cc_final: 0.7431 (mpp)
REVERT: A  140 PHE cc_start: 0.9000 (m-80) cc_final: 0.8332 (m-80)
REVERT: A  259 TYR cc_start: 0.9029 (m-80) cc_final: 0.7759 (m-80)
REVERT: A  262 PHE cc_start: 0.9571 (m-80) cc_final: 0.8990 (m-80)
REVERT: A  319 GLU cc_start: 0.8912 (tp30) cc_final: 0.8172 (tp30)
REVERT: A  326 PHE cc_start: 0.8860 (m-80) cc_final: 0.8565 (m-80)
REVERT: A  360 PHE cc_start: 0.9081 (t80) cc_final: 0.8848 (t80)
REVERT: A  387 TYR cc_start: 0.8452 (t80) cc_final: 0.8238 (t80)
REVERT: A  408 TYR cc_start: 0.8923 (t80) cc_final: 0.8574 (t80)
REVERT: A  438 ILE cc_start: 0.9175 (mm) cc_final: 0.8890 (mm)
REVERT: A  454 ILE cc_start: 0.9838 (mt) cc_final: 0.9233 (mt)
REVERT: A  460 LYS cc_start: 0.9751 (tppp) cc_final: 0.9501 (tptp)
REVERT: A  559 TYR cc_start: 0.8596 (m-80) cc_final: 0.8219 (m-80)
REVERT: A  564 PHE cc_start: 0.9572 (m-80) cc_final: 0.9018 (m-80)
REVERT: A  580 LEU cc_start: 0.9210 (mm) cc_final: 0.8851 (pp)
REVERT: A  588 LEU cc_start: 0.9150 (mt) cc_final: 0.8789 (mt)
REVERT: A  676 ARG cc_start: 0.9545 (mmm160) cc_final: 0.9240 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.0728
  time to fit residues: 12.6669
Evaluate side-chains
  99 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 30 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 69 optimal weight:    0.0870
   chunk 32 optimal weight:    0.7980
   chunk 63 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 13 optimal weight:    0.8980
   chunk 54 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    2.3562

-------------------------------------------------------------------------------
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 290 GLN
** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.077170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.048546 restraints weight = 29920.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.050321 restraints weight = 21624.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.051669 restraints weight = 17083.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.052632 restraints weight = 14348.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.053366 restraints weight = 12624.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3081
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3081 r_free = 0.3081    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 = 0.3081 r_free = 0.3081    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3081
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.7510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6141  Z= 0.178
  Angle     :  0.662   6.666   8286  Z= 0.348
  Chirality :  0.042   0.150    892
  Planarity :  0.004   0.047   1060
  Dihedral  :  7.286 133.492    814
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 16.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.30), residues: 733
  helix:  0.97 (0.27), residues: 360
  sheet: -0.46 (0.47), residues: 102
  loop : -0.32 (0.37), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 309 
 TYR   0.016   0.002   TYR A 113 
 PHE   0.020   0.002   PHE A 449 
 TRP   0.032   0.003   TRP A 523 
 HIS   0.005   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 6141)
  covalent geometry    : angle       0.66217 ( 8286)
  hydrogen bonds       : bond        0.03717 (  326)
  hydrogen bonds       : angle       5.27584 (  915)

*********************** 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
  126 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.9390 (mp0) cc_final: 0.9081 (mp0)
REVERT: A   92 ARG cc_start: 0.9608 (tpt170) cc_final: 0.9160 (mmm160)
REVERT: A  140 PHE cc_start: 0.9048 (m-80) cc_final: 0.8328 (m-80)
REVERT: A  220 PHE cc_start: 0.9339 (p90) cc_final: 0.8949 (p90)
REVERT: A  259 TYR cc_start: 0.8911 (m-80) cc_final: 0.7849 (m-80)
REVERT: A  262 PHE cc_start: 0.9579 (m-80) cc_final: 0.8962 (m-80)
REVERT: A  295 MET cc_start: 0.9458 (pmm) cc_final: 0.9255 (pmm)
REVERT: A  299 VAL cc_start: 0.4564 (t) cc_final: 0.4190 (t)
REVERT: A  304 GLU cc_start: 0.9238 (mp0) cc_final: 0.8821 (mp0)
REVERT: A  308 THR cc_start: 0.9849 (p) cc_final: 0.9507 (p)
REVERT: A  319 GLU cc_start: 0.8936 (tp30) cc_final: 0.8220 (tp30)
REVERT: A  360 PHE cc_start: 0.9111 (t80) cc_final: 0.8863 (t80)
REVERT: A  387 TYR cc_start: 0.8520 (t80) cc_final: 0.8311 (t80)
REVERT: A  408 TYR cc_start: 0.8977 (t80) cc_final: 0.8609 (t80)
REVERT: A  438 ILE cc_start: 0.8788 (mm) cc_final: 0.8412 (mm)
REVERT: A  439 TYR cc_start: 0.9085 (p90) cc_final: 0.8426 (p90)
REVERT: A  454 ILE cc_start: 0.9715 (mt) cc_final: 0.9130 (mt)
REVERT: A  460 LYS cc_start: 0.9786 (tppp) cc_final: 0.9522 (tptp)
REVERT: A  559 TYR cc_start: 0.8423 (m-80) cc_final: 0.8140 (m-80)
REVERT: A  580 LEU cc_start: 0.9259 (mm) cc_final: 0.8937 (pp)
REVERT: A  588 LEU cc_start: 0.9228 (mt) cc_final: 0.8951 (mt)
REVERT: A  676 ARG cc_start: 0.9595 (mmm160) cc_final: 0.9218 (mmm160)
REVERT: A  701 TRP cc_start: 0.9502 (m-90) cc_final: 0.9173 (m-90)
REVERT: A  750 PHE cc_start: 0.9402 (m-10) cc_final: 0.9012 (m-10)
REVERT: A  755 VAL cc_start: 0.8464 (t) cc_final: 0.8249 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.0883
  time to fit residues: 14.3713
Evaluate side-chains
  98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 52 optimal weight:    7.9990
   chunk 50 optimal weight:    0.5980
   chunk 72 optimal weight:   20.0000
   chunk 6 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   chunk 69 optimal weight:    9.9990
   chunk 22 optimal weight:    0.7980
   chunk 36 optimal weight:    7.9990
   chunk 38 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    2.0786

-------------------------------------------------------------------------------
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 429 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 = 0.3581 r_free = 0.3581 target = 0.077488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.048996 restraints weight = 30365.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.050723 restraints weight = 22157.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.051996 restraints weight = 17599.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.053029 restraints weight = 14856.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.053820 restraints weight = 13051.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
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:        4 |
|-----------------------------------------------------------------------------|
|-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: 0.8113
moved from start:          0.7743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6141  Z= 0.161
  Angle     :  0.657   6.674   8286  Z= 0.345
  Chirality :  0.042   0.161    892
  Planarity :  0.004   0.031   1060
  Dihedral  :  7.234 132.580    814
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 16.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.30), residues: 733
  helix:  0.90 (0.27), residues: 362
  sheet: -0.43 (0.47), residues: 100
  loop : -0.34 (0.37), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 257 
 TYR   0.030   0.002   TYR A 263 
 PHE   0.028   0.002   PHE A 639 
 TRP   0.023   0.002   TRP A 523 
 HIS   0.005   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 6141)
  covalent geometry    : angle       0.65748 ( 8286)
  hydrogen bonds       : bond        0.03744 (  326)
  hydrogen bonds       : angle       5.25716 (  915)

*********************** 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
  127 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.9415 (mp0) cc_final: 0.9107 (mp0)
REVERT: A   92 ARG cc_start: 0.9619 (tpt170) cc_final: 0.9181 (mmm160)
REVERT: A  140 PHE cc_start: 0.8988 (m-80) cc_final: 0.8316 (m-80)
REVERT: A  220 PHE cc_start: 0.9363 (p90) cc_final: 0.8972 (p90)
REVERT: A  262 PHE cc_start: 0.9646 (m-80) cc_final: 0.9139 (m-80)
REVERT: A  304 GLU cc_start: 0.9339 (mp0) cc_final: 0.8862 (mp0)
REVERT: A  319 GLU cc_start: 0.8875 (tp30) cc_final: 0.7987 (tp30)
REVERT: A  323 MET cc_start: 0.9226 (mmp) cc_final: 0.9014 (mmm)
REVERT: A  360 PHE cc_start: 0.9123 (t80) cc_final: 0.8849 (t80)
REVERT: A  387 TYR cc_start: 0.8633 (t80) cc_final: 0.8396 (t80)
REVERT: A  403 LEU cc_start: 0.9783 (tp) cc_final: 0.9412 (pp)
REVERT: A  408 TYR cc_start: 0.8993 (t80) cc_final: 0.8641 (t80)
REVERT: A  438 ILE cc_start: 0.8727 (mm) cc_final: 0.8181 (mm)
REVERT: A  439 TYR cc_start: 0.9001 (p90) cc_final: 0.8365 (p90)
REVERT: A  454 ILE cc_start: 0.9725 (mt) cc_final: 0.9102 (mt)
REVERT: A  460 LYS cc_start: 0.9779 (tppp) cc_final: 0.9494 (tptp)
REVERT: A  465 PHE cc_start: 0.9593 (t80) cc_final: 0.9386 (t80)
REVERT: A  466 ASN cc_start: 0.9593 (t0) cc_final: 0.9261 (t0)
REVERT: A  559 TYR cc_start: 0.8246 (m-80) cc_final: 0.7733 (m-80)
REVERT: A  580 LEU cc_start: 0.9288 (mm) cc_final: 0.9004 (pp)
REVERT: A  588 LEU cc_start: 0.9209 (mt) cc_final: 0.8864 (mt)
REVERT: A  676 ARG cc_start: 0.9589 (mmm160) cc_final: 0.9197 (mmm160)
REVERT: A  714 MET cc_start: 0.6787 (mmm) cc_final: 0.6317 (tpp)
REVERT: A  750 PHE cc_start: 0.9428 (m-80) cc_final: 0.9197 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0848
  time to fit residues: 13.9545
Evaluate side-chains
  95 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 59 optimal weight:    8.9990
   chunk 2 optimal weight:    0.5980
   chunk 72 optimal weight:   20.0000
   chunk 6 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    2.5188

-------------------------------------------------------------------------------
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 429 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 = 0.3549 r_free = 0.3549 target = 0.076442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.047731 restraints weight = 30916.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.049485 restraints weight = 22006.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.050756 restraints weight = 17366.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.051780 restraints weight = 14603.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.052481 restraints weight = 12819.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3056
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    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 = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3056
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.8075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6141  Z= 0.184
  Angle     :  0.683   6.710   8286  Z= 0.360
  Chirality :  0.042   0.139    892
  Planarity :  0.004   0.033   1060
  Dihedral  :  7.385 132.202    814
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 18.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.30), residues: 733
  helix:  0.67 (0.26), residues: 363
  sheet: -0.72 (0.47), residues: 102
  loop : -0.30 (0.37), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 309 
 TYR   0.026   0.002   TYR A 263 
 PHE   0.021   0.002   PHE A 449 
 TRP   0.036   0.003   TRP A 523 
 HIS   0.006   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 6141)
  covalent geometry    : angle       0.68333 ( 8286)
  hydrogen bonds       : bond        0.03856 (  326)
  hydrogen bonds       : angle       5.45211 (  915)

*********************** 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
  122 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.9415 (mp0) cc_final: 0.9104 (mp0)
REVERT: A   22 TRP cc_start: 0.9281 (m100) cc_final: 0.9024 (m100)
REVERT: A   92 ARG cc_start: 0.9614 (tpt170) cc_final: 0.9182 (mmm160)
REVERT: A  140 PHE cc_start: 0.9043 (m-80) cc_final: 0.8333 (m-80)
REVERT: A  220 PHE cc_start: 0.9292 (p90) cc_final: 0.8753 (p90)
REVERT: A  262 PHE cc_start: 0.9669 (m-80) cc_final: 0.9293 (m-80)
REVERT: A  304 GLU cc_start: 0.9354 (mp0) cc_final: 0.8814 (mp0)
REVERT: A  360 PHE cc_start: 0.9137 (t80) cc_final: 0.8899 (t80)
REVERT: A  364 MET cc_start: 0.8358 (mpp) cc_final: 0.8145 (mpp)
REVERT: A  387 TYR cc_start: 0.8548 (t80) cc_final: 0.8316 (t80)
REVERT: A  403 LEU cc_start: 0.9797 (tp) cc_final: 0.9438 (pp)
REVERT: A  408 TYR cc_start: 0.9018 (t80) cc_final: 0.8775 (t80)
REVERT: A  439 TYR cc_start: 0.8975 (p90) cc_final: 0.8559 (p90)
REVERT: A  454 ILE cc_start: 0.9765 (mt) cc_final: 0.9199 (mt)
REVERT: A  459 GLU cc_start: 0.9415 (mm-30) cc_final: 0.9196 (mm-30)
REVERT: A  460 LYS cc_start: 0.9790 (tppp) cc_final: 0.9532 (tptp)
REVERT: A  465 PHE cc_start: 0.9634 (t80) cc_final: 0.9375 (t80)
REVERT: A  466 ASN cc_start: 0.9628 (t0) cc_final: 0.9289 (t0)
REVERT: A  486 LEU cc_start: 0.8292 (mt) cc_final: 0.8025 (mt)
REVERT: A  559 TYR cc_start: 0.8229 (m-80) cc_final: 0.7654 (m-80)
REVERT: A  580 LEU cc_start: 0.9299 (mm) cc_final: 0.9053 (pp)
REVERT: A  588 LEU cc_start: 0.9252 (mt) cc_final: 0.8903 (mt)
REVERT: A  676 ARG cc_start: 0.9618 (mmm160) cc_final: 0.9206 (mmm160)
REVERT: A  701 TRP cc_start: 0.9492 (m-90) cc_final: 0.9190 (m-90)
REVERT: A  750 PHE cc_start: 0.9460 (m-80) cc_final: 0.9071 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0817
  time to fit residues: 12.9863
Evaluate side-chains
  98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 70 optimal weight:    8.9990
   chunk 38 optimal weight:    9.9990
   chunk 18 optimal weight:    8.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 679 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 = 0.3615 r_free = 0.3615 target = 0.079315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.049546 restraints weight = 29465.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.051417 restraints weight = 21214.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.052778 restraints weight = 16690.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.053918 restraints weight = 13996.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.054550 restraints weight = 12207.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.8213

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= 0.120
  Angle     :  0.630   6.898   8286  Z= 0.328
  Chirality :  0.042   0.145    892
  Planarity :  0.004   0.030   1060
  Dihedral  :  7.091 134.523    814
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.31), residues: 733
  helix:  1.01 (0.27), residues: 362
  sheet: -0.31 (0.49), residues: 102
  loop : -0.21 (0.38), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 155 
 TYR   0.019   0.002   TYR A 263 
 PHE   0.019   0.002   PHE A 360 
 TRP   0.064   0.003   TRP A 523 
 HIS   0.004   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 6141)
  covalent geometry    : angle       0.62978 ( 8286)
  hydrogen bonds       : bond        0.03528 (  326)
  hydrogen bonds       : angle       5.12930 (  915)

********************** 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
  130 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.9412 (mp0) cc_final: 0.9113 (mp0)
REVERT: A   22 TRP cc_start: 0.9292 (m100) cc_final: 0.8787 (m100)
REVERT: A   92 ARG cc_start: 0.9632 (tpt170) cc_final: 0.9186 (mmm160)
REVERT: A  140 PHE cc_start: 0.8965 (m-80) cc_final: 0.8337 (m-80)
REVERT: A  220 PHE cc_start: 0.9253 (p90) cc_final: 0.8769 (p90)
REVERT: A  262 PHE cc_start: 0.9625 (m-80) cc_final: 0.9277 (m-80)
REVERT: A  304 GLU cc_start: 0.9327 (mp0) cc_final: 0.8751 (mp0)
REVERT: A  308 THR cc_start: 0.9796 (p) cc_final: 0.9578 (p)
REVERT: A  319 GLU cc_start: 0.8852 (tp30) cc_final: 0.8138 (tp30)
REVERT: A  364 MET cc_start: 0.8173 (mpp) cc_final: 0.7818 (mpp)
REVERT: A  371 MET cc_start: 0.9469 (tmm) cc_final: 0.9263 (tmm)
REVERT: A  387 TYR cc_start: 0.8563 (t80) cc_final: 0.8355 (t80)
REVERT: A  408 TYR cc_start: 0.9003 (t80) cc_final: 0.8765 (t80)
REVERT: A  436 LEU cc_start: 0.9591 (tp) cc_final: 0.9322 (tp)
REVERT: A  438 ILE cc_start: 0.9007 (mm) cc_final: 0.8572 (mm)
REVERT: A  439 TYR cc_start: 0.9242 (p90) cc_final: 0.8639 (p90)
REVERT: A  454 ILE cc_start: 0.9736 (mt) cc_final: 0.9145 (mt)
REVERT: A  460 LYS cc_start: 0.9754 (tppp) cc_final: 0.9468 (tptp)
REVERT: A  465 PHE cc_start: 0.9572 (t80) cc_final: 0.9334 (t80)
REVERT: A  466 ASN cc_start: 0.9569 (t0) cc_final: 0.9198 (t0)
REVERT: A  559 TYR cc_start: 0.8188 (m-80) cc_final: 0.7582 (m-80)
REVERT: A  580 LEU cc_start: 0.9322 (mm) cc_final: 0.9073 (pp)
REVERT: A  588 LEU cc_start: 0.9213 (mt) cc_final: 0.8877 (mt)
REVERT: A  676 ARG cc_start: 0.9585 (mmm160) cc_final: 0.9193 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0805
  time to fit residues: 13.7583
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  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 36 optimal weight:   10.0000
   chunk 15 optimal weight:    6.9990
   chunk 2 optimal weight:    0.7980
   chunk 18 optimal weight:    9.9990
   chunk 72 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.1384

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.079411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.049959 restraints weight = 29333.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.051849 restraints weight = 21115.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.053173 restraints weight = 16561.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.054292 restraints weight = 13889.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.055084 restraints weight = 12140.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.8383

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= 0.121
  Angle     :  0.622   7.062   8286  Z= 0.323
  Chirality :  0.041   0.148    892
  Planarity :  0.004   0.030   1060
  Dihedral  :  7.093 132.430    814
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.31), residues: 733
  helix:  1.03 (0.27), residues: 362
  sheet: -0.24 (0.48), residues: 105
  loop : -0.10 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 248 
 TYR   0.019   0.002   TYR A 263 
 PHE   0.015   0.002   PHE A 360 
 TRP   0.070   0.004   TRP A 523 
 HIS   0.004   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 6141)
  covalent geometry    : angle       0.62150 ( 8286)
  hydrogen bonds       : bond        0.03433 (  326)
  hydrogen bonds       : angle       5.10978 (  915)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1154.10 seconds
wall clock time: 20 minutes 38.88 seconds (1238.88 seconds total)