Starting phenix.real_space_refine
on Sat Aug 23 21:55:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t2r_40985/08_2025/8t2r_40985.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t2r_40985/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t2r_40985/08_2025/8t2r_40985.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t2r_40985/08_2025/8t2r_40985.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t2r_40985/08_2025/8t2r_40985.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t2r_40985/08_2025/8t2r_40985.map"
  }
  resolution = 3.1
  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=   0.028
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.19, per 1000 atoms: 0.28
  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: 1.19
  Conformation dependent library (CDL) restraints added in 439.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 2.70
  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: 4.02

  Time building geometry restraints manager: 1.73 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:             4.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     18.520
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.030
-------------------------------------------------------------------------------
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 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: -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
 ARG   0.005   0.001   ARG D 217 
 TYR   0.029   0.003   TYR D 350 
 PHE   0.018   0.003   PHE D 221 
 TRP   0.009   0.002   TRP D 328 
 HIS   0.003   0.001   HIS D 284 

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

*********************** 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  : 0.277 
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: 0.1711
  time to fit residues: 9.0701
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  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    2.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.173043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.115926 restraints weight = 46867.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 2.25
r_work: 0.2994 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2980
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2980 r_free = 0.2980    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 = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2979
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.046  16531  Z= 0.367
  Angle     :  0.768  11.103  25066  Z= 0.383
  Chirality :  0.042   0.323   3232
  Planarity :  0.006   0.080   1108
  Dihedral  : 25.142 175.883   8912
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  3.93 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 21.90 %
    Favored  : 74.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -0.63 (0.39), residues: 394
  helix:  0.31 (0.29), residues: 272
  sheet: -0.81 (1.05), residues: 20
  loop : -2.17 (0.54), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 353 
 TYR   0.023   0.002   TYR D 385 
 PHE   0.013   0.002   PHE D 145 
 TRP   0.011   0.002   TRP D 136 
 HIS   0.004   0.002   HIS D 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00703 (16531)
  covalent geometry    : angle       0.76797 (25066)
  hydrogen bonds       : bond        0.08266 (  644)
  hydrogen bonds       : angle       3.63265 ( 1305)

*********************** 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
  35 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 27
  time to evaluate  : 0.229 
Fit side-chains
REVERT: D   88 ARG cc_start: 0.7531 (ttm110) cc_final: 0.6896 (mtm110)
REVERT: D  216 LYS cc_start: 0.8721 (tmtt) cc_final: 0.8391 (tttt)
REVERT: D  247 ARG cc_start: 0.8097 (ttp80) cc_final: 0.7307 (ttm170)
  outliers start: 8
  outliers final: 6
  residues processed: 31
  average time/residue: 0.1651
  time to fit residues: 7.4094
Evaluate side-chains
  33 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 27
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  379 THR
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 25 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 78 optimal weight:   10.0000
   chunk 86 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    1.9186

-------------------------------------------------------------------------------
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 = 0.4076 r_free = 0.4076 target = 0.176062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.130206 restraints weight = 53233.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 1.47
r_work: 0.3066 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3022
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3022
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  16531  Z= 0.267
  Angle     :  0.671   8.512  25066  Z= 0.337
  Chirality :  0.037   0.313   3232
  Planarity :  0.005   0.078   1108
  Dihedral  : 25.004 177.119   8912
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  3.66 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 22.19 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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:  0.22 (0.41), residues: 394
  helix:  0.99 (0.31), residues: 273
  sheet: -0.96 (0.96), residues: 22
  loop : -1.88 (0.57), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 247 
 TYR   0.022   0.002   TYR D 385 
 PHE   0.013   0.002   PHE D 145 
 TRP   0.009   0.002   TRP D 136 
 HIS   0.003   0.001   HIS D 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 (16531)
  covalent geometry    : angle       0.67148 (25066)
  hydrogen bonds       : bond        0.07160 (  644)
  hydrogen bonds       : angle       3.38200 ( 1305)

*********************** 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
  39 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 30
  time to evaluate  : 0.247 
Fit side-chains
REVERT: D   88 ARG cc_start: 0.7515 (ttm110) cc_final: 0.6824 (mtm110)
REVERT: D  197 ASN cc_start: 0.6580 (t0) cc_final: 0.6188 (t0)
REVERT: D  216 LYS cc_start: 0.8680 (tmtt) cc_final: 0.8410 (tttt)
REVERT: D  236 MET cc_start: 0.6058 (ppp) cc_final: 0.5822 (ttp)
REVERT: D  247 ARG cc_start: 0.7934 (ttp80) cc_final: 0.7628 (tmm-80)
  outliers start: 9
  outliers final: 7
  residues processed: 36
  average time/residue: 0.1524
  time to fit residues: 7.9876
Evaluate side-chains
  36 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 29
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 26 optimal weight:    0.3980
   chunk 74 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4119 r_free = 0.4119 target = 0.180169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.137280 restraints weight = 50426.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 1.11
r_work: 0.3140 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3018
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3018 r_free = 0.3018    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 = 0.3018 r_free = 0.3018    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3018
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.2445

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= 0.141
  Angle     :  0.581   7.153  25066  Z= 0.294
  Chirality :  0.032   0.314   3232
  Planarity :  0.005   0.083   1108
  Dihedral  : 24.857 175.687   8912
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  3.14 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 21.61 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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 (0.43), residues: 394
  helix:  1.52 (0.32), residues: 273
  sheet: -0.97 (0.98), residues: 22
  loop : -1.78 (0.59), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 247 
 TYR   0.017   0.002   TYR D 385 
 PHE   0.010   0.001   PHE D 145 
 TRP   0.007   0.001   TRP D 136 
 HIS   0.002   0.001   HIS D 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (16531)
  covalent geometry    : angle       0.58088 (25066)
  hydrogen bonds       : bond        0.06108 (  644)
  hydrogen bonds       : angle       3.17599 ( 1305)

*********************** 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
  45 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 34
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: D   88 ARG cc_start: 0.7387 (ttm110) cc_final: 0.6772 (mtm110)
REVERT: D  197 ASN cc_start: 0.6425 (t0) cc_final: 0.6104 (t0)
REVERT: D  216 LYS cc_start: 0.8687 (tmtt) cc_final: 0.8425 (tttt)
REVERT: D  236 MET cc_start: 0.5948 (ppp) cc_final: 0.5649 (ttp)
REVERT: D  247 ARG cc_start: 0.7922 (ttp80) cc_final: 0.7618 (tmm-80)
REVERT: D  396 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7819 (pptt)
  outliers start: 11
  outliers final: 8
  residues processed: 41
  average time/residue: 0.1613
  time to fit residues: 9.3146
Evaluate side-chains
  40 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
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  310 TRP
Chi-restraints excluded: chain D residue  312 VAL
Chi-restraints excluded: chain D residue  396 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 67 optimal weight:   10.0000
   chunk 12 optimal weight:    0.8980
   chunk 91 optimal weight:   10.0000
   chunk 85 optimal weight:    2.9990
   overall best weight:    1.7586

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.177952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.130048 restraints weight = 44949.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 1.67
r_work: 0.3062 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2851
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2851 r_free = 0.2851    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 = 0.2851 r_free = 0.2851    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2851
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.2570

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= 0.246
  Angle     :  0.637   7.386  25066  Z= 0.320
  Chirality :  0.035   0.279   3232
  Planarity :  0.005   0.082   1108
  Dihedral  : 24.818 177.082   8912
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  3.93 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 21.33 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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:  0.95 (0.43), residues: 394
  helix:  1.64 (0.31), residues: 272
  sheet: -0.83 (0.98), residues: 22
  loop : -1.91 (0.58), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 353 
 TYR   0.022   0.002   TYR D 385 
 PHE   0.011   0.002   PHE D 145 
 TRP   0.007   0.001   TRP D 136 
 HIS   0.003   0.001   HIS D 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 (16531)
  covalent geometry    : angle       0.63749 (25066)
  hydrogen bonds       : bond        0.07034 (  644)
  hydrogen bonds       : angle       3.21909 ( 1305)

*********************** 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
  43 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 30
  time to evaluate  : 0.161 
Fit side-chains
REVERT: D   88 ARG cc_start: 0.7288 (ttm110) cc_final: 0.6595 (mtm110)
REVERT: D  197 ASN cc_start: 0.6613 (t0) cc_final: 0.6197 (t0)
REVERT: D  216 LYS cc_start: 0.8722 (tmtt) cc_final: 0.8471 (tttt)
REVERT: D  236 MET cc_start: 0.5999 (ppp) cc_final: 0.5521 (ttp)
REVERT: D  247 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7630 (tmm-80)
REVERT: D  396 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8066 (pttp)
  outliers start: 13
  outliers final: 9
  residues processed: 40
  average time/residue: 0.1306
  time to fit residues: 7.4123
Evaluate side-chains
  40 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 30
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 79 optimal weight:   20.0000
   chunk 37 optimal weight:    0.7980
   chunk 68 optimal weight:   10.0000
   chunk 15 optimal weight:    0.2980
   chunk 27 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    1.1982

-------------------------------------------------------------------------------
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 = 0.4107 r_free = 0.4107 target = 0.179015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.139523 restraints weight = 58946.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3656 rms_B_bonded: 1.10
r_work: 0.3121 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2920
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2920 r_free = 0.2920    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2920 r_free = 0.2920    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2920
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.2659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  16531  Z= 0.182
  Angle     :  0.599   7.125  25066  Z= 0.301
  Chirality :  0.033   0.272   3232
  Planarity :  0.005   0.080   1108
  Dihedral  : 24.803 176.337   8912
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  3.14 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 22.19 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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:  1.16 (0.43), residues: 394
  helix:  1.81 (0.31), residues: 273
  sheet: -0.87 (0.98), residues: 22
  loop : -1.84 (0.58), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 247 
 TYR   0.020   0.002   TYR D 385 
 PHE   0.010   0.001   PHE D 145 
 TRP   0.007   0.001   TRP D 136 
 HIS   0.003   0.001   HIS D 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (16531)
  covalent geometry    : angle       0.59944 (25066)
  hydrogen bonds       : bond        0.06571 (  644)
  hydrogen bonds       : angle       3.13871 ( 1305)

*********************** 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
  40 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 30
  time to evaluate  : 0.153 
Fit side-chains
REVERT: D   88 ARG cc_start: 0.7379 (ttm110) cc_final: 0.6701 (mtm110)
REVERT: D  197 ASN cc_start: 0.6638 (t0) cc_final: 0.6242 (t0)
REVERT: D  216 LYS cc_start: 0.8691 (tmtt) cc_final: 0.8457 (tttt)
REVERT: D  236 MET cc_start: 0.6063 (ppp) cc_final: 0.5616 (ttp)
REVERT: D  247 ARG cc_start: 0.7980 (ttp80) cc_final: 0.7625 (tmm-80)
  outliers start: 10
  outliers final: 9
  residues processed: 38
  average time/residue: 0.1383
  time to fit residues: 7.6063
Evaluate side-chains
  38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 29
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
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  399 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 91 optimal weight:   10.0000
   chunk 84 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    0.8980
   chunk 63 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 81 optimal weight:   20.0000
   chunk 72 optimal weight:    5.9990
   overall best weight:    2.9788

-------------------------------------------------------------------------------
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 = 0.4068 r_free = 0.4068 target = 0.175573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.132524 restraints weight = 58656.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 1.50
r_work: 0.3073 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2814
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2814 r_free = 0.2814    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 = 0.2814 r_free = 0.2814    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2814
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053  16531  Z= 0.383
  Angle     :  0.748   7.875  25066  Z= 0.373
  Chirality :  0.041   0.293   3232
  Planarity :  0.006   0.078   1108
  Dihedral  : 24.858 176.989   8912
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  4.45 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 21.33 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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:  0.77 (0.42), residues: 394
  helix:  1.49 (0.31), residues: 272
  sheet: -0.71 (0.96), residues: 22
  loop : -1.95 (0.57), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 353 
 TYR   0.026   0.002   TYR D 385 
 PHE   0.013   0.002   PHE D 145 
 TRP   0.007   0.002   TRP D 136 
 HIS   0.005   0.001   HIS D 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00734 (16531)
  covalent geometry    : angle       0.74784 (25066)
  hydrogen bonds       : bond        0.08338 (  644)
  hydrogen bonds       : angle       3.40511 ( 1305)

*********************** 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
  39 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 27
  time to evaluate  : 0.248 
Fit side-chains
REVERT: D   88 ARG cc_start: 0.7427 (ttm110) cc_final: 0.6756 (mtm110)
REVERT: D  216 LYS cc_start: 0.8687 (tmtt) cc_final: 0.8438 (tttt)
REVERT: D  247 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7682 (tmm-80)
  outliers start: 12
  outliers final: 12
  residues processed: 37
  average time/residue: 0.1146
  time to fit residues: 6.2659
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  : 0.211 
-------------------------------------------------------------------------------
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  167 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  310 TRP
Chi-restraints excluded: chain D residue  312 VAL
Chi-restraints excluded: chain D residue  379 THR
Chi-restraints excluded: chain D residue  399 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 89 optimal weight:   20.0000
   chunk 8 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0570
   chunk 80 optimal weight:   20.0000
   chunk 52 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    1.0104

-------------------------------------------------------------------------------
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 = 0.4120 r_free = 0.4120 target = 0.180539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.130414 restraints weight = 43879.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 1.67
r_work: 0.3140 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3039
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3039 r_free = 0.3039    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 = 0.3039 r_free = 0.3039    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3039
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.2939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  16531  Z= 0.159
  Angle     :  0.585   7.186  25066  Z= 0.295
  Chirality :  0.032   0.257   3232
  Planarity :  0.005   0.080   1108
  Dihedral  : 24.775 176.341   8912
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  2.88 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 22.19 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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:  1.20 (0.42), residues: 394
  helix:  1.83 (0.31), residues: 273
  sheet: -1.09 (0.92), residues: 22
  loop : -1.73 (0.59), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 247 
 TYR   0.020   0.002   TYR D 385 
 PHE   0.010   0.001   PHE D 145 
 TRP   0.006   0.001   TRP D 357 
 HIS   0.001   0.001   HIS D 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (16531)
  covalent geometry    : angle       0.58509 (25066)
  hydrogen bonds       : bond        0.06377 (  644)
  hydrogen bonds       : angle       3.16428 ( 1305)

*********************** 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
  38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 29
  time to evaluate  : 0.264 
Fit side-chains
REVERT: D    7 MET cc_start: 0.7649 (tpt) cc_final: 0.7328 (tpt)
REVERT: D   88 ARG cc_start: 0.7219 (ttm110) cc_final: 0.6635 (mtm110)
REVERT: D  197 ASN cc_start: 0.6515 (t0) cc_final: 0.6126 (t0)
REVERT: D  216 LYS cc_start: 0.8728 (tmtt) cc_final: 0.8476 (tttt)
REVERT: D  236 MET cc_start: 0.5830 (ppp) cc_final: 0.5369 (ttp)
REVERT: D  247 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7613 (tmm-80)
  outliers start: 9
  outliers final: 9
  residues processed: 36
  average time/residue: 0.1184
  time to fit residues: 6.4110
Evaluate side-chains
  38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 29
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
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  379 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 80 optimal weight:   20.0000
   chunk 61 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 86 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 55 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    1.2382

-------------------------------------------------------------------------------
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 = 0.4112 r_free = 0.4112 target = 0.179802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.133333 restraints weight = 48581.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 1.21
r_work: 0.3128 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2896
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2896
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.2980

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= 0.187
  Angle     :  0.595   7.118  25066  Z= 0.300
  Chirality :  0.032   0.249   3232
  Planarity :  0.005   0.079   1108
  Dihedral  : 24.720 177.071   8912
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  3.93 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 22.48 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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:  1.32 (0.43), residues: 394
  helix:  1.96 (0.31), residues: 272
  sheet: -1.06 (0.93), residues: 22
  loop : -1.80 (0.59), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 247 
 TYR   0.022   0.002   TYR D 385 
 PHE   0.009   0.002   PHE D 145 
 TRP   0.006   0.001   TRP D 136 
 HIS   0.002   0.001   HIS D 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (16531)
  covalent geometry    : angle       0.59548 (25066)
  hydrogen bonds       : bond        0.06572 (  644)
  hydrogen bonds       : angle       3.17140 ( 1305)

*********************** 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
  37 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.256 
Fit side-chains
REVERT: D    7 MET cc_start: 0.7648 (tpt) cc_final: 0.7373 (tpt)
REVERT: D   88 ARG cc_start: 0.7226 (ttm110) cc_final: 0.6615 (mtm110)
REVERT: D  197 ASN cc_start: 0.6573 (t0) cc_final: 0.6174 (t0)
REVERT: D  216 LYS cc_start: 0.8702 (tmtt) cc_final: 0.8467 (tttt)
REVERT: D  236 MET cc_start: 0.5871 (ppp) cc_final: 0.5468 (ttp)
REVERT: D  247 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7627 (tmm-80)
  outliers start: 9
  outliers final: 9
  residues processed: 35
  average time/residue: 0.1447
  time to fit residues: 7.3781
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  : 0.257 
-------------------------------------------------------------------------------
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  379 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 43 optimal weight:   10.0000
   chunk 37 optimal weight:    0.8980
   chunk 80 optimal weight:   20.0000
   chunk 52 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 64 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    1.8784

-------------------------------------------------------------------------------
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 = 0.4100 r_free = 0.4100 target = 0.178704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.128989 restraints weight = 44048.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 1.70
r_work: 0.3099 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2865
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2865 r_free = 0.2865    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 = 0.2865 r_free = 0.2865    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2865
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  16531  Z= 0.253
  Angle     :  0.638   7.420  25066  Z= 0.320
  Chirality :  0.035   0.260   3232
  Planarity :  0.005   0.079   1108
  Dihedral  : 24.723 177.277   8912
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  4.45 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 21.61 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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:  1.21 (0.42), residues: 394
  helix:  1.88 (0.31), residues: 272
  sheet: -1.03 (0.91), residues: 22
  loop : -1.86 (0.59), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 353 
 TYR   0.025   0.002   TYR D 385 
 PHE   0.011   0.002   PHE D 145 
 TRP   0.006   0.001   TRP D 136 
 HIS   0.003   0.001   HIS D 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 (16531)
  covalent geometry    : angle       0.63813 (25066)
  hydrogen bonds       : bond        0.07156 (  644)
  hydrogen bonds       : angle       3.23036 ( 1305)

********************** 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
  40 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 29
  time to evaluate  : 0.264 
Fit side-chains
REVERT: D   88 ARG cc_start: 0.7240 (ttm110) cc_final: 0.6597 (mtm110)
REVERT: D  197 ASN cc_start: 0.6583 (t0) cc_final: 0.6139 (t0)
REVERT: D  216 LYS cc_start: 0.8690 (tmtt) cc_final: 0.8461 (tttt)
REVERT: D  247 ARG cc_start: 0.8071 (ttp80) cc_final: 0.7633 (tmm-80)
  outliers start: 11
  outliers final: 10
  residues processed: 38
  average time/residue: 0.1451
  time to fit residues: 8.0831
Evaluate side-chains
  39 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 29
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
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  379 THR
Chi-restraints excluded: chain D residue  399 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 2 optimal weight:    0.3980
   chunk 87 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 14 optimal weight:    0.4980
   chunk 54 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0040
   chunk 53 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 9 optimal weight:    0.7980
   chunk 59 optimal weight:   10.0000
   overall best weight:    0.7394

-------------------------------------------------------------------------------
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 = 0.4130 r_free = 0.4130 target = 0.181581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 92)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.130303 restraints weight = 41128.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 1.91
r_work: 0.3144 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3036
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    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 = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3036
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.3130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  16531  Z= 0.144
  Angle     :  0.571   7.017  25066  Z= 0.288
  Chirality :  0.031   0.240   3232
  Planarity :  0.005   0.081   1108
  Dihedral  : 24.681 175.710   8912
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  3.14 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 23.34 %
    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 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:  1.39 (0.43), residues: 394
  helix:  1.98 (0.31), residues: 273
  sheet: -1.10 (0.93), residues: 22
  loop : -1.69 (0.61), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 240 
 TYR   0.017   0.001   TYR D 385 
 PHE   0.009   0.001   PHE D 145 
 TRP   0.006   0.001   TRP D 357 
 HIS   0.001   0.000   HIS D 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (16531)
  covalent geometry    : angle       0.57051 (25066)
  hydrogen bonds       : bond        0.06220 (  644)
  hydrogen bonds       : angle       3.11685 ( 1305)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3663.65 seconds
wall clock time: 63 minutes 37.23 seconds (3817.23 seconds total)