Starting phenix.real_space_refine
on Fri Jun 13 11:01:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t2r_40985/06_2025/8t2r_40985.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t2r_40985/06_2025/8t2r_40985.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t2r_40985/06_2025/8t2r_40985.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t2r_40985/06_2025/8t2r_40985.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t2r_40985/06_2025/8t2r_40985.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t2r_40985/06_2025/8t2r_40985.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.028
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
     Ca     13      9.91       5
     P     552      5.49       5
     S      21      5.16       5
     C    7314      2.51       5
     N    2782      2.21       5
     O    4381      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 15063
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "D"
      Number of atoms: 3184
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 388, 3142
          Classifications: {'peptide': 388}
          Link IDs: {'PTRANS': 10, 'TRANS': 377}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 388, 3142
          Classifications: {'peptide': 388}
          Link IDs: {'PTRANS': 10, 'TRANS': 377}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 3149
    Chain: "A"
      Number of atoms: 140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 140
          Classifications: {'RNA': 7}
          Modifications used: {'rna2p_pyr': 3, 'rna3p_pyr': 4}
          Link IDs: {'rna2p': 3, 'rna3p': 3}
    Chain: "B"
      Number of atoms: 11724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 545, 11724
          Classifications: {'RNA': 545}
          Modifications used: {'rna2p_pur': 39, 'rna2p_pyr': 10, 'rna3p_pur': 291, 'rna3p_pyr': 205}
          Link IDs: {'rna2p': 48, 'rna3p': 496}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 15
          Unusual residues: {' CA': 13, 'NH4': 2}
          Classifications: {'undetermined': 15}
          Link IDs: {None: 14}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N  AARG D 347 " occ=0.25
      ... (20 atoms not shown)
      pdb=" NH2BARG D 347 " occ=0.75
    residue:
      pdb=" N  AGLN D 359 " occ=0.72
      ... (16 atoms not shown)
      pdb=" NE2BGLN D 359 " occ=0.28
    residue:
      pdb=" N  AARG D 382 " occ=0.67
      ... (20 atoms not shown)
      pdb=" NH2BARG D 382 " occ=0.33
    residue:
      pdb=" N  AARG D 407 " occ=0.48
      ... (20 atoms not shown)
      pdb=" NH2BARG D 407 " occ=0.52
  Time building chain proxies: 11.54, per 1000 atoms: 0.77
  Number of scatterers: 15063
  At special positions: 0
  Unit cell: (97.904, 134.196, 160.36, 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)
     Ca     13     19.99
     S      21     16.00
     P     552     15.00
     O    4381      8.00
     N    2782      7.00
     C    7314      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: 3.93
  Conformation dependent library (CDL) restraints added in 965.5 milliseconds
  

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  736

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 2 sheets defined
      70.9% alpha, 5.9% beta
      177 base pairs and 312 stacking pairs defined.
    Time for finding SS restraints: 7.66
  Creating SS restraints...
    Processing helix  chain 'D' and resid 4 through 11
    Processing helix  chain 'D' and resid 12 through 27
    Processing helix  chain 'D' and resid 36 through 57
      removed outlier: 6.619A  pdb=" N   GLU D  49 " --> pdb=" O   ALA D  45 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   THR D  50 " --> pdb=" O   LYS D  46 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 84 through 99
    Processing helix  chain 'D' and resid 101 through 106
    Processing helix  chain 'D' and resid 118 through 132
      removed outlier: 3.601A  pdb=" N   ALA D 122 " --> pdb=" O   CYS D 118 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 144 through 149
    Processing helix  chain 'D' and resid 150 through 162
      removed outlier: 3.589A  pdb=" N   LEU D 154 " --> pdb=" O   ASN D 150 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 164 through 177
      removed outlier: 3.681A  pdb=" N   ILE D 168 " --> pdb=" O   ASP D 164 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 218
      removed outlier: 4.304A  pdb=" N   LEU D 201 " --> pdb=" O   ASN D 197 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   LEU D 210 " --> pdb=" O   MET D 206 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 234 through 252
    Processing helix  chain 'D' and resid 291 through 306
    Processing helix  chain 'D' and resid 313 through 333
    Processing helix  chain 'D' and resid 337 through 361
      removed outlier: 3.658A  pdb=" N   LYS D 361 " --> pdb=" O   TRP D 357 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 362 through 374
    Processing helix  chain 'D' and resid 376 through 385
      removed outlier: 4.381A  pdb=" N  AARG D 382 " --> pdb=" O   ASN D 378 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 389 through 396
      removed outlier: 4.032A  pdb=" N   LYS D 396 " --> pdb=" O   TYR D 392 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 397 through 403
    Processing helix  chain 'D' and resid 404 through 411
    Processing helix  chain 'D' and resid 415 through 424
    Processing sheet with id=AA1, first strand: chain 'D' and resid 220 through 224
      removed outlier: 4.374A  pdb=" N   ASN D 220 " --> pdb=" O   MET D 231 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   CYS D 228 " --> pdb=" O   ILE D 140 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 275 through 279

    205 hydrogen bonds defined for protein.
    613 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      439 hydrogen bonds
      692 hydrogen bond angles
      0 basepair planarities
      177 basepair parallelities
      312 stacking parallelities
  Total time for adding SS restraints: 9.55

  Time building geometry restraints manager: 4.55 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: 1878
        1.33 -     1.45: 7659
        1.45 -     1.57: 5863
        1.57 -     1.69: 1096
        1.69 -     1.82: 35
  Bond restraints: 16531
  Sorted by residual:
  bond pdb=" C   ASP D 265 "
       pdb=" N   ARG D 266 "
    ideal  model  delta    sigma   weight residual
    1.335  1.250  0.084 3.04e-02 1.08e+03 7.69e+00
  bond pdb=" CB  MET D 354 "
       pdb=" CG  MET D 354 "
    ideal  model  delta    sigma   weight residual
    1.520  1.461  0.059 3.00e-02 1.11e+03 3.90e+00
  bond pdb=" SD  MET D 354 "
       pdb=" CE  MET D 354 "
    ideal  model  delta    sigma   weight residual
    1.791  1.743  0.048 2.50e-02 1.60e+03 3.75e+00
  bond pdb=" C2'   A B 370 "
       pdb=" O2'   A B 370 "
    ideal  model  delta    sigma   weight residual
    1.420  1.395  0.025 1.50e-02 4.44e+03 2.82e+00
  bond pdb=" SD  MET D 337 "
       pdb=" CE  MET D 337 "
    ideal  model  delta    sigma   weight residual
    1.791  1.749  0.042 2.50e-02 1.60e+03 2.78e+00
  ... (remaining 16526 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.84: 24936
        4.84 -     9.68: 125
        9.68 -    14.52: 4
       14.52 -    19.36: 0
       19.36 -    24.20: 1
  Bond angle restraints: 25066
  Sorted by residual:
  angle pdb=" C   ASP D 265 "
        pdb=" N   ARG D 266 "
        pdb=" CA  ARG D 266 "
      ideal   model   delta    sigma   weight residual
     121.95  146.15  -24.20 3.74e+00 7.15e-02 4.19e+01
  angle pdb=" C   ALA D 225 "
        pdb=" N   ASP D 226 "
        pdb=" CA  ASP D 226 "
      ideal   model   delta    sigma   weight residual
     122.61  131.23   -8.62 1.56e+00 4.11e-01 3.05e+01
  angle pdb=" O3'   C B 206 "
        pdb=" C3'   C B 206 "
        pdb=" C2'   C B 206 "
      ideal   model   delta    sigma   weight residual
     113.70  121.28   -7.58 1.50e+00 4.44e-01 2.56e+01
  angle pdb=" C3'   A B  67 "
        pdb=" O3'   A B  67 "
        pdb=" P     U B  68 "
      ideal   model   delta    sigma   weight residual
     120.20  127.49   -7.29 1.50e+00 4.44e-01 2.36e+01
  angle pdb=" O3'   U B  46 "
        pdb=" C3'   U B  46 "
        pdb=" C2'   U B  46 "
      ideal   model   delta    sigma   weight residual
     113.70  120.78   -7.08 1.50e+00 4.44e-01 2.23e+01
  ... (remaining 25061 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.34: 8939
       35.34 -    70.68: 1356
       70.68 -   106.02: 158
      106.02 -   141.36: 8
      141.36 -   176.70: 9
  Dihedral angle restraints: 10470
    sinusoidal: 9325
      harmonic: 1145
  Sorted by residual:
  dihedral pdb=" CA  PRO D 100 "
           pdb=" C   PRO D 100 "
           pdb=" N   ILE D 101 "
           pdb=" CA  ILE D 101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -128.31  -51.69     0      5.00e+00 4.00e-02 1.07e+02
  dihedral pdb=" O4'   C B 138 "
           pdb=" C1'   C B 138 "
           pdb=" N1    C B 138 "
           pdb=" C2    C B 138 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   16.70 -176.70     1      1.50e+01 4.44e-03 8.53e+01
  dihedral pdb=" O4'   U B 361 "
           pdb=" C1'   U B 361 "
           pdb=" N1    U B 361 "
           pdb=" C2    U B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   48.56  151.44     1      1.50e+01 4.44e-03 8.01e+01
  ... (remaining 10467 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 2960
       0.074 -    0.148: 241
       0.148 -    0.221: 18
       0.221 -    0.295: 6
       0.295 -    0.369: 7
  Chirality restraints: 3232
  Sorted by residual:
  chirality pdb=" C1'   A B  51 "
            pdb=" O4'   A B  51 "
            pdb=" C2'   A B  51 "
            pdb=" N9    A B  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.09    0.37 2.00e-01 2.50e+01 3.40e+00
  chirality pdb=" C3'   U B  46 "
            pdb=" C4'   U B  46 "
            pdb=" O3'   U B  46 "
            pdb=" C2'   U B  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.13   -0.35 2.00e-01 2.50e+01 3.09e+00
  chirality pdb=" C3'   G B 348 "
            pdb=" C4'   G B 348 "
            pdb=" O3'   G B 348 "
            pdb=" C2'   G B 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.40   -0.35 2.00e-01 2.50e+01 3.01e+00
  ... (remaining 3229 not shown)

  Planarity restraints: 1108
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D  99 "   -0.057 5.00e-02 4.00e+02   8.63e-02 1.19e+01
        pdb=" N   PRO D 100 "    0.149 5.00e-02 4.00e+02
        pdb=" CA  PRO D 100 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO D 100 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B  51 "    0.038 2.00e-02 2.50e+03   1.81e-02 9.05e+00
        pdb=" N9    A B  51 "   -0.045 2.00e-02 2.50e+03
        pdb=" C8    A B  51 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7    A B  51 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    A B  51 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    A B  51 "    0.004 2.00e-02 2.50e+03
        pdb=" N6    A B  51 "    0.009 2.00e-02 2.50e+03
        pdb=" N1    A B  51 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    A B  51 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    A B  51 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    A B  51 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B 436 "    0.037 2.00e-02 2.50e+03   1.93e-02 8.37e+00
        pdb=" N1    U B 436 "   -0.040 2.00e-02 2.50e+03
        pdb=" C2    U B 436 "   -0.007 2.00e-02 2.50e+03
        pdb=" O2    U B 436 "   -0.000 2.00e-02 2.50e+03
        pdb=" N3    U B 436 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    U B 436 "    0.008 2.00e-02 2.50e+03
        pdb=" O4    U B 436 "    0.012 2.00e-02 2.50e+03
        pdb=" C5    U B 436 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    U B 436 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1105 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 1629
        2.72 -     3.26: 12266
        3.26 -     3.81: 32606
        3.81 -     4.35: 39407
        4.35 -     4.90: 50689
  Nonbonded interactions: 136597
  Sorted by model distance:
  nonbonded pdb=" O2'   A B 370 "
            pdb=" O4'   G B 371 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" O2'   G B 136 "
            pdb=" OP1   U B 148 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OG  SER D 415 "
            pdb=" OD2 ASP D 418 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" OP2   A B 137 "
            pdb=" O2'   A B 147 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OG  SER D 110 "
            pdb=" OD2 ASP D 211 "
     model   vdw
     2.295 3.040
  ... (remaining 136592 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             4.710
  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:             0.020
  Extract box with map and model:          0.670
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     47.060
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.060
  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:             0.010
  Load rotamer database and sin/cos tables:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   55.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
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      :  0.006   0.084  16531  Z= 0.294
  Angle     :  0.956  24.199  25066  Z= 0.456
  Chirality :  0.045   0.369   3232
  Planarity :  0.007   0.086   1108
  Dihedral  : 25.029 176.698   9734
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  3.14 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 23.34 %
    Favored  : 75.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.52 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.34), residues: 394
  helix: -0.97 (0.26), residues: 272
  sheet: -1.11 (1.04), residues: 20
  loop : -2.29 (0.49), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP D 328 
 HIS   0.003   0.001   HIS D 284 
 PHE   0.018   0.003   PHE D 221 
 TYR   0.029   0.003   TYR D 350 
 ARG   0.005   0.001   ARG D 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13901 (  644)
  hydrogen bonds       : angle       5.28168 ( 1305)
  covalent geometry    : bond        0.00561 (16531)
  covalent geometry    : angle       0.95636 (25066)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.665 
Fit side-chains
REVERT: D  197 ASN cc_start: 0.6283 (t0) cc_final: 0.5914 (t0)
REVERT: D  216 LYS cc_start: 0.8625 (tmtt) cc_final: 0.8217 (tttt)
REVERT: D  236 MET cc_start: 0.5233 (ppp) cc_final: 0.4107 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.3454
  time to fit residues: 18.4727
Evaluate side-chains
  33 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:   10.0000
   chunk 69 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 37 optimal weight:    0.5980
   chunk 72 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 43 optimal weight:   10.0000
   chunk 53 optimal weight:    3.9990
   chunk 83 optimal weight:   20.0000
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.175555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.128924 restraints weight = 49645.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 1.24
r_work: 0.3062 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3044
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3044 r_free = 0.3044    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3043
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  16531  Z= 0.242
  Angle     :  0.672   9.854  25066  Z= 0.339
  Chirality :  0.036   0.313   3232
  Planarity :  0.005   0.080   1108
  Dihedral  : 25.092 176.494   8912
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  3.40 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 22.77 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.40), residues: 394
  helix:  0.59 (0.30), residues: 273
  sheet: -1.00 (1.02), residues: 22
  loop : -1.91 (0.55), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D 136 
 HIS   0.005   0.001   HIS D 284 
 PHE   0.012   0.002   PHE D 145 
 TYR   0.021   0.002   TYR D 385 
 ARG   0.007   0.001   ARG D 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06905 (  644)
  hydrogen bonds       : angle       3.43673 ( 1305)
  covalent geometry    : bond        0.00460 (16531)
  covalent geometry    : angle       0.67244 (25066)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.738 
Fit side-chains
REVERT: D   88 ARG cc_start: 0.7444 (ttm110) cc_final: 0.6863 (mtm110)
REVERT: D  197 ASN cc_start: 0.6416 (t0) cc_final: 0.6075 (t0)
REVERT: D  216 LYS cc_start: 0.8685 (tmtt) cc_final: 0.8405 (tttt)
REVERT: D  247 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7602 (tmm-80)
  outliers start: 6
  outliers final: 6
  residues processed: 32
  average time/residue: 0.3323
  time to fit residues: 15.5893
Evaluate side-chains
  34 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain D residue  206 MET
Chi-restraints excluded: chain D residue  232 VAL
Chi-restraints excluded: chain D residue  302 MET
Chi-restraints excluded: chain D residue  310 TRP
Chi-restraints excluded: chain D residue  399 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 67 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9980
   chunk 75 optimal weight:    6.9990
   chunk 76 optimal weight:   20.0000
   chunk 89 optimal weight:   20.0000
   chunk 58 optimal weight:    8.9990
   chunk 49 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
D  63 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.176697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.132924 restraints weight = 52803.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 1.31
r_work: 0.3076 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2854
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2854
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  16531  Z= 0.272
  Angle     :  0.675   8.525  25066  Z= 0.338
  Chirality :  0.037   0.287   3232
  Planarity :  0.005   0.079   1108
  Dihedral  : 24.954 177.488   8912
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  3.66 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 21.04 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.42), residues: 394
  helix:  1.22 (0.31), residues: 273
  sheet: -0.90 (0.99), residues: 22
  loop : -1.84 (0.57), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP D 136 
 HIS   0.004   0.001   HIS D 107 
 PHE   0.012   0.002   PHE D 145 
 TYR   0.023   0.002   TYR D 385 
 ARG   0.005   0.001   ARG D 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07374 (  644)
  hydrogen bonds       : angle       3.34303 ( 1305)
  covalent geometry    : bond        0.00521 (16531)
  covalent geometry    : angle       0.67522 (25066)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 26
  time to evaluate  : 0.659 
Fit side-chains
REVERT: D   88 ARG cc_start: 0.7378 (ttm110) cc_final: 0.6730 (mtm110)
REVERT: D  197 ASN cc_start: 0.6657 (t0) cc_final: 0.6214 (t0)
REVERT: D  216 LYS cc_start: 0.8660 (tmtt) cc_final: 0.8343 (tttt)
  outliers start: 12
  outliers final: 8
  residues processed: 33
  average time/residue: 0.2886
  time to fit residues: 14.3121
Evaluate side-chains
  33 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 25
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  206 MET
Chi-restraints excluded: chain D residue  232 VAL
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  302 MET
Chi-restraints excluded: chain D residue  310 TRP
Chi-restraints excluded: chain D residue  312 VAL
Chi-restraints excluded: chain D residue  379 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 48 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 90 optimal weight:   30.0000
   chunk 2 optimal weight:    7.9990
   chunk 74 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 5 optimal weight:   20.0000
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
D  63 GLN
** D 314 ASN ** 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 = 0.4082 r_free = 0.4082 target = 0.176879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.127549 restraints weight = 41630.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 1.67
r_work: 0.3065 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2815
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2815 r_free = 0.2815    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2815 r_free = 0.2815    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2815
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.2678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  16531  Z= 0.311
  Angle     :  0.696   7.900  25066  Z= 0.349
  Chirality :  0.038   0.273   3232
  Planarity :  0.005   0.081   1108
  Dihedral  : 24.909 177.080   8912
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  4.19 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 21.33 %
    Favored  : 73.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.42), residues: 394
  helix:  1.37 (0.31), residues: 272
  sheet: -0.84 (0.96), residues: 22
  loop : -1.94 (0.58), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D 136 
 HIS   0.004   0.001   HIS D 107 
 PHE   0.014   0.002   PHE D 145 
 TYR   0.024   0.002   TYR D 385 
 ARG   0.007   0.001   ARG D 353 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07656 (  644)
  hydrogen bonds       : angle       3.35607 ( 1305)
  covalent geometry    : bond        0.00594 (16531)
  covalent geometry    : angle       0.69603 (25066)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 26
  time to evaluate  : 0.696 
Fit side-chains
REVERT: D   88 ARG cc_start: 0.7298 (ttm110) cc_final: 0.6639 (mtm110)
REVERT: D  216 LYS cc_start: 0.8656 (tmtt) cc_final: 0.8378 (tttt)
REVERT: D  236 MET cc_start: 0.5981 (ttp) cc_final: 0.5760 (ttp)
REVERT: D  396 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8239 (pttm)
  outliers start: 15
  outliers final: 12
  residues processed: 37
  average time/residue: 0.2930
  time to fit residues: 16.1494
Evaluate side-chains
  40 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 27
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   37 TYR
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  206 MET
Chi-restraints excluded: chain D residue  232 VAL
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  265 ASP
Chi-restraints excluded: chain D residue  302 MET
Chi-restraints excluded: chain D residue  310 TRP
Chi-restraints excluded: chain D residue  312 VAL
Chi-restraints excluded: chain D residue  379 THR
Chi-restraints excluded: chain D residue  396 LYS
Chi-restraints excluded: chain D residue  399 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 21 optimal weight:    0.4980
   chunk 85 optimal weight:    2.9990
   chunk 59 optimal weight:   10.0000
   chunk 3 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 76 optimal weight:   20.0000
   chunk 23 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 43 optimal weight:    9.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
D  63 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.179497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.136815 restraints weight = 46557.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 1.14
r_work: 0.3132 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2960
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2960
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  16531  Z= 0.211
  Angle     :  0.626   7.341  25066  Z= 0.315
  Chirality :  0.034   0.276   3232
  Planarity :  0.005   0.080   1108
  Dihedral  : 24.849 177.065   8912
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  3.66 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 22.19 %
    Favored  : 73.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.42), residues: 394
  helix:  1.60 (0.31), residues: 273
  sheet: -0.88 (0.94), residues: 22
  loop : -1.82 (0.58), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 136 
 HIS   0.003   0.001   HIS D 107 
 PHE   0.011   0.002   PHE D 145 
 TYR   0.021   0.002   TYR D 385 
 ARG   0.003   0.000   ARG D 353 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06801 (  644)
  hydrogen bonds       : angle       3.21788 ( 1305)
  covalent geometry    : bond        0.00397 (16531)
  covalent geometry    : angle       0.62616 (25066)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 28
  time to evaluate  : 0.662 
Fit side-chains
REVERT: D   88 ARG cc_start: 0.7388 (ttm110) cc_final: 0.6740 (mtm110)
REVERT: D  197 ASN cc_start: 0.6603 (t0) cc_final: 0.6242 (t0)
REVERT: D  216 LYS cc_start: 0.8646 (tmtt) cc_final: 0.8421 (tttt)
REVERT: D  247 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7671 (tmm-80)
REVERT: D  396 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.7963 (pttp)
  outliers start: 12
  outliers final: 10
  residues processed: 37
  average time/residue: 0.3073
  time to fit residues: 16.4471
Evaluate side-chains
  38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 27
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   37 TYR
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  206 MET
Chi-restraints excluded: chain D residue  232 VAL
Chi-restraints excluded: chain D residue  265 ASP
Chi-restraints excluded: chain D residue  302 MET
Chi-restraints excluded: chain D residue  310 TRP
Chi-restraints excluded: chain D residue  312 VAL
Chi-restraints excluded: chain D residue  379 THR
Chi-restraints excluded: chain D residue  396 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 58 optimal weight:    8.9990
   chunk 79 optimal weight:   20.0000
   chunk 40 optimal weight:    6.9990
   chunk 8 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 59 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
D  63 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.178224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.130830 restraints weight = 52290.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 1.58
r_work: 0.3085 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2836
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2836
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.2814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  16531  Z= 0.257
  Angle     :  0.649   7.533  25066  Z= 0.326
  Chirality :  0.036   0.271   3232
  Planarity :  0.005   0.080   1108
  Dihedral  : 24.812 177.429   8912
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  3.93 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 22.48 %
    Favored  : 72.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.42), residues: 394
  helix:  1.70 (0.31), residues: 272
  sheet: -0.85 (0.93), residues: 22
  loop : -1.90 (0.58), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 136 
 HIS   0.003   0.001   HIS D 107 
 PHE   0.011   0.002   PHE D 145 
 TYR   0.024   0.002   TYR D 385 
 ARG   0.004   0.001   ARG D 353 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07248 (  644)
  hydrogen bonds       : angle       3.25977 ( 1305)
  covalent geometry    : bond        0.00490 (16531)
  covalent geometry    : angle       0.64855 (25066)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 26
  time to evaluate  : 0.631 
Fit side-chains
REVERT: D   88 ARG cc_start: 0.7329 (ttm110) cc_final: 0.6673 (mtm110)
REVERT: D  197 ASN cc_start: 0.6696 (t0) cc_final: 0.6298 (t0)
REVERT: D  216 LYS cc_start: 0.8672 (tmtt) cc_final: 0.8393 (tttt)
REVERT: D  247 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7675 (tmm-80)
REVERT: D  396 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8093 (pttp)
  outliers start: 13
  outliers final: 12
  residues processed: 36
  average time/residue: 0.3228
  time to fit residues: 16.9851
Evaluate side-chains
  39 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 26
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   37 TYR
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  156 THR
Chi-restraints excluded: chain D residue  206 MET
Chi-restraints excluded: chain D residue  232 VAL
Chi-restraints excluded: chain D residue  265 ASP
Chi-restraints excluded: chain D residue  302 MET
Chi-restraints excluded: chain D residue  310 TRP
Chi-restraints excluded: chain D residue  312 VAL
Chi-restraints excluded: chain D residue  379 THR
Chi-restraints excluded: chain D residue  396 LYS
Chi-restraints excluded: chain D residue  399 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 4 optimal weight:   30.0000
   chunk 10 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 58 optimal weight:    7.9990
   chunk 62 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 24 optimal weight:    0.5980
   chunk 41 optimal weight:    6.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
D  63 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.179662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.134598 restraints weight = 49090.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3584 rms_B_bonded: 1.22
r_work: 0.3115 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2866
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2866
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.2829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  16531  Z= 0.187
  Angle     :  0.618   7.114  25066  Z= 0.311
  Chirality :  0.033   0.265   3232
  Planarity :  0.005   0.078   1108
  Dihedral  : 24.835 176.844   8912
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  3.66 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 22.77 %
    Favored  : 72.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.43), residues: 394
  helix:  1.79 (0.31), residues: 273
  sheet: -0.83 (0.94), residues: 22
  loop : -1.76 (0.59), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 136 
 HIS   0.002   0.001   HIS D 107 
 PHE   0.011   0.002   PHE D 145 
 TYR   0.021   0.002   TYR D 385 
 ARG   0.004   0.000   ARG D 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06958 (  644)
  hydrogen bonds       : angle       3.20396 ( 1305)
  covalent geometry    : bond        0.00353 (16531)
  covalent geometry    : angle       0.61764 (25066)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 26
  time to evaluate  : 0.746 
Fit side-chains
REVERT: D   88 ARG cc_start: 0.7363 (ttm110) cc_final: 0.6711 (mtm110)
REVERT: D  197 ASN cc_start: 0.6654 (t0) cc_final: 0.6189 (t0)
REVERT: D  216 LYS cc_start: 0.8639 (tmtt) cc_final: 0.8415 (tttt)
REVERT: D  247 ARG cc_start: 0.8071 (ttp80) cc_final: 0.7667 (tmm-80)
REVERT: D  396 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8042 (pttp)
  outliers start: 12
  outliers final: 11
  residues processed: 35
  average time/residue: 0.3432
  time to fit residues: 17.5161
Evaluate side-chains
  38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 26
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   37 TYR
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  156 THR
Chi-restraints excluded: chain D residue  206 MET
Chi-restraints excluded: chain D residue  232 VAL
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  265 ASP
Chi-restraints excluded: chain D residue  302 MET
Chi-restraints excluded: chain D residue  310 TRP
Chi-restraints excluded: chain D residue  312 VAL
Chi-restraints excluded: chain D residue  396 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 5 optimal weight:    0.3980
   chunk 46 optimal weight:    6.9990
   chunk 86 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 41 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 85 optimal weight:    2.9990
   chunk 66 optimal weight:   20.0000
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
D  63 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.177834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.127694 restraints weight = 51849.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.84
r_work: 0.3064 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2845
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2845
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.2927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  16531  Z= 0.271
  Angle     :  0.661   7.521  25066  Z= 0.332
  Chirality :  0.036   0.261   3232
  Planarity :  0.005   0.080   1108
  Dihedral  : 24.793 177.330   8912
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  4.19 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 22.77 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.42), residues: 394
  helix:  1.78 (0.31), residues: 272
  sheet: -0.89 (0.90), residues: 22
  loop : -1.90 (0.59), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 136 
 HIS   0.003   0.001   HIS D 107 
 PHE   0.011   0.002   PHE D 145 
 TYR   0.025   0.002   TYR D 385 
 ARG   0.004   0.001   ARG D 353 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07426 (  644)
  hydrogen bonds       : angle       3.27340 ( 1305)
  covalent geometry    : bond        0.00518 (16531)
  covalent geometry    : angle       0.66147 (25066)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 27
  time to evaluate  : 0.662 
Fit side-chains
REVERT: D   88 ARG cc_start: 0.7234 (ttm110) cc_final: 0.6590 (mtm110)
REVERT: D  216 LYS cc_start: 0.8695 (tmtt) cc_final: 0.8393 (tttt)
REVERT: D  396 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8113 (pttp)
  outliers start: 13
  outliers final: 12
  residues processed: 37
  average time/residue: 0.3118
  time to fit residues: 16.8654
Evaluate side-chains
  39 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 26
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   37 TYR
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  156 THR
Chi-restraints excluded: chain D residue  206 MET
Chi-restraints excluded: chain D residue  232 VAL
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  265 ASP
Chi-restraints excluded: chain D residue  302 MET
Chi-restraints excluded: chain D residue  310 TRP
Chi-restraints excluded: chain D residue  312 VAL
Chi-restraints excluded: chain D residue  396 LYS
Chi-restraints excluded: chain D residue  399 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   chunk 85 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 41 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
D  63 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.180804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.137766 restraints weight = 65708.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 1.18
r_work: 0.3149 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2929
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2929
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.3049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  16531  Z= 0.166
  Angle     :  0.586   7.251  25066  Z= 0.294
  Chirality :  0.032   0.254   3232
  Planarity :  0.005   0.081   1108
  Dihedral  : 24.723 176.343   8912
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  2.88 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 22.77 %
    Favored  : 72.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.43), residues: 394
  helix:  1.96 (0.31), residues: 273
  sheet: -1.01 (0.91), residues: 22
  loop : -1.68 (0.61), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 136 
 HIS   0.001   0.000   HIS D 109 
 PHE   0.010   0.001   PHE D 145 
 TYR   0.018   0.002   TYR D 385 
 ARG   0.006   0.000   ARG D 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06358 (  644)
  hydrogen bonds       : angle       3.13482 ( 1305)
  covalent geometry    : bond        0.00310 (16531)
  covalent geometry    : angle       0.58568 (25066)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 28
  time to evaluate  : 1.964 
Fit side-chains
REVERT: D    7 MET cc_start: 0.7688 (tpt) cc_final: 0.7334 (tpt)
REVERT: D   88 ARG cc_start: 0.7267 (ttm110) cc_final: 0.6676 (mtp180)
REVERT: D  197 ASN cc_start: 0.6551 (t0) cc_final: 0.6138 (t0)
REVERT: D  216 LYS cc_start: 0.8741 (tmtt) cc_final: 0.8493 (tttt)
REVERT: D  396 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.7879 (pptt)
  outliers start: 12
  outliers final: 8
  residues processed: 36
  average time/residue: 0.5043
  time to fit residues: 28.7209
Evaluate side-chains
  37 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 2.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   37 TYR
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  156 THR
Chi-restraints excluded: chain D residue  206 MET
Chi-restraints excluded: chain D residue  232 VAL
Chi-restraints excluded: chain D residue  310 TRP
Chi-restraints excluded: chain D residue  312 VAL
Chi-restraints excluded: chain D residue  396 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   chunk 49 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
D  63 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.175611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.128976 restraints weight = 54304.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 1.81
r_work: 0.3046 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3030
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3030
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.3118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051  16531  Z= 0.381
  Angle     :  0.746   7.757  25066  Z= 0.370
  Chirality :  0.040   0.295   3232
  Planarity :  0.006   0.079   1108
  Dihedral  : 24.787 176.888   8912
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  4.45 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 22.19 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.42), residues: 394
  helix:  1.64 (0.31), residues: 272
  sheet: -0.87 (0.91), residues: 22
  loop : -1.96 (0.57), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP D 136 
 HIS   0.005   0.001   HIS D 107 
 PHE   0.012   0.002   PHE D 145 
 TYR   0.028   0.002   TYR D 385 
 ARG   0.006   0.001   ARG D 353 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08424 (  644)
  hydrogen bonds       : angle       3.39567 ( 1305)
  covalent geometry    : bond        0.00734 (16531)
  covalent geometry    : angle       0.74590 (25066)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 27
  time to evaluate  : 0.644 
Fit side-chains
REVERT: D   88 ARG cc_start: 0.7459 (ttm110) cc_final: 0.6842 (mtm110)
REVERT: D  216 LYS cc_start: 0.8650 (tmtt) cc_final: 0.8408 (tttt)
REVERT: D  247 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7675 (tmm-80)
REVERT: D  396 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8142 (pttp)
  outliers start: 11
  outliers final: 8
  residues processed: 36
  average time/residue: 0.3907
  time to fit residues: 20.5286
Evaluate side-chains
  36 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 27
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   37 TYR
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  156 THR
Chi-restraints excluded: chain D residue  206 MET
Chi-restraints excluded: chain D residue  232 VAL
Chi-restraints excluded: chain D residue  310 TRP
Chi-restraints excluded: chain D residue  312 VAL
Chi-restraints excluded: chain D residue  396 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 43 optimal weight:   10.0000
   chunk 84 optimal weight:   10.0000
   chunk 30 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 3 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
D  63 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.179898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.131674 restraints weight = 51945.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 1.45
r_work: 0.3101 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2987
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2987 r_free = 0.2987    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2987 r_free = 0.2987    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2987
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.3137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  16531  Z= 0.198
  Angle     :  0.614   7.375  25066  Z= 0.309
  Chirality :  0.033   0.246   3232
  Planarity :  0.005   0.080   1108
  Dihedral  : 24.728 176.860   8912
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  3.14 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 22.48 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.42), residues: 394
  helix:  1.80 (0.31), residues: 273
  sheet: -0.95 (0.91), residues: 22
  loop : -1.74 (0.59), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 136 
 HIS   0.002   0.001   HIS D 107 
 PHE   0.011   0.002   PHE D 145 
 TYR   0.020   0.002   TYR D 385 
 ARG   0.006   0.000   ARG D 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06717 (  644)
  hydrogen bonds       : angle       3.21281 ( 1305)
  covalent geometry    : bond        0.00374 (16531)
  covalent geometry    : angle       0.61363 (25066)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8097.81 seconds
wall clock time: 143 minutes 1.57 seconds (8581.57 seconds total)