Starting phenix.real_space_refine
on Tue Mar  3 19:14:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ctl_26994/03_2026/8ctl_26994_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ctl_26994/03_2026/8ctl_26994.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/8ctl_26994/03_2026/8ctl_26994.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ctl_26994/03_2026/8ctl_26994.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ctl_26994/03_2026/8ctl_26994_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ctl_26994/03_2026/8ctl_26994_neut.cif"
  }
  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: 5
    Type Number    sf(0)   Gaussians
     P     233      5.49       5
     S      21      5.16       5
     C    4257      2.51       5
     N    1486      2.21       5
     O    2141      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8138
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "D"
      Number of atoms: 3209
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 401, 3209
          Classifications: {'peptide': 401}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 382}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 3937
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 3937
          Classifications: {'RNA': 184}
          Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 11, 'rna3p_pur': 89, 'rna3p_pyr': 69}
          Link IDs: {'rna2p': 26, 'rna3p': 157}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 579
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 579
          Classifications: {'DNA': 29}
          Link IDs: {'rna3p': 28}
    Chain: "B"
      Number of atoms: 413
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 413
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
  Time building chain proxies: 1.96, per 1000 atoms: 0.24
  Number of scatterers: 8138
  At special positions: 0
  Unit cell: (89.88, 103.79, 131.61, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      21     16.00
     P     233     15.00
     O    2141      8.00
     N    1486      7.00
     C    4257      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 130.1 milliseconds
  

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  752

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 6 sheets defined
      29.9% alpha, 18.2% beta
      75 base pairs and 130 stacking pairs defined.
    Time for finding SS restraints: 1.33
  Creating SS restraints...
    Processing helix  chain 'D' and resid 20 through 29
      removed outlier: 3.755A  pdb=" N   LEU D  27 " --> pdb=" O   VAL D  23 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 89 through 108
    Processing helix  chain 'D' and resid 109 through 121
    Processing helix  chain 'D' and resid 163 through 181
    Processing helix  chain 'D' and resid 297 through 313
      Proline residue:  D 304  - end of helix
    Processing helix  chain 'D' and resid 323 through 333
    Processing helix  chain 'D' and resid 338 through 340
      No H-bonds generated for 'chain 'D' and resid 338 through 340'
    Processing helix  chain 'D' and resid 341 through 349
      removed outlier: 3.658A  pdb=" N   CYS D 345 " --> pdb=" O   LEU D 341 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 408 through 416
    Processing helix  chain 'D' and resid 417 through 422
    Processing helix  chain 'D' and resid 480 through 482
      No H-bonds generated for 'chain 'D' and resid 480 through 482'
    Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 14
      removed outlier: 4.626A  pdb=" N   VAL D   6 " --> pdb=" O   LEU D  14 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   TYR D   5 " --> pdb=" O   ILE D  42 " (cutoff:3.500A)
      removed outlier: 7.545A  pdb=" N   LEU D  44 " --> pdb=" O   TYR D   5 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   ILE D   7 " --> pdb=" O   LEU D  44 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   THR D  41 " --> pdb=" O   VAL D  35 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 318 through 322
      removed outlier: 6.256A  pdb=" N   VAL D 189 " --> pdb=" O   CYS D 319 " (cutoff:3.500A)
      removed outlier: 7.271A  pdb=" N   THR D 321 " --> pdb=" O   VAL D 189 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   LEU D 191 " --> pdb=" O   THR D 321 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   MET D  68 " --> pdb=" O   ALA D  81 " (cutoff:3.500A)
      removed outlier: 6.067A  pdb=" N   THR D  72 " --> pdb=" O   SER D  77 " (cutoff:3.500A)
      removed outlier: 6.031A  pdb=" N   SER D  77 " --> pdb=" O   THR D  72 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   VAL D 367 " --> pdb=" O   GLN D  82 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   MET D 366 " --> pdb=" O   TYR D 494 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 128 through 131
    Processing sheet with id=AA4, first strand: chain 'D' and resid 378 through 380
    Processing sheet with id=AA5, first strand: chain 'D' and resid 387 through 388
      removed outlier: 6.045A  pdb=" N   TYR D 387 " --> pdb=" O   VAL D 394 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 476 through 478
      removed outlier: 6.535A  pdb=" N   TYR D 468 " --> pdb=" O   SER D 458 " (cutoff:3.500A)
      removed outlier: 4.764A  pdb=" N   SER D 458 " --> pdb=" O   TYR D 468 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   VAL D 470 " --> pdb=" O   SER D 456 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   VAL D 446 " --> pdb=" O   TYR D 484 " (cutoff:3.500A)
      removed outlier: 5.742A  pdb=" N   TYR D 484 " --> pdb=" O   VAL D 446 " (cutoff:3.500A)

    114 hydrogen bonds defined for protein.
    324 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      190 hydrogen bonds
      356 hydrogen bond angles
      0 basepair planarities
      75 basepair parallelities
      130 stacking parallelities
  Total time for adding SS restraints: 1.43

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 785
        1.30 -     1.43: 3479
        1.43 -     1.56: 4025
        1.56 -     1.69: 460
        1.69 -     1.81: 33
  Bond restraints: 8782
  Sorted by residual:
  bond pdb=" CA  ARG D 131 "
       pdb=" C   ARG D 131 "
    ideal  model  delta    sigma   weight residual
    1.526  1.456  0.070 1.20e-02 6.94e+03 3.38e+01
  bond pdb=" CA  ALA D 381 "
       pdb=" C   ALA D 381 "
    ideal  model  delta    sigma   weight residual
    1.526  1.452  0.074 1.30e-02 5.92e+03 3.20e+01
  bond pdb=" CA  ARG D 371 "
       pdb=" C   ARG D 371 "
    ideal  model  delta    sigma   weight residual
    1.525  1.460  0.065 1.28e-02 6.10e+03 2.55e+01
  bond pdb=" N   GLN D 465 "
       pdb=" CA  GLN D 465 "
    ideal  model  delta    sigma   weight residual
    1.461  1.402  0.059 1.20e-02 6.94e+03 2.46e+01
  bond pdb=" C   ARG D 131 "
       pdb=" O   ARG D 131 "
    ideal  model  delta    sigma   weight residual
    1.235  1.178  0.056 1.14e-02 7.69e+03 2.45e+01
  ... (remaining 8777 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.17: 11629
        2.17 -     4.35: 1182
        4.35 -     6.52: 112
        6.52 -     8.70: 21
        8.70 -    10.87: 13
  Bond angle restraints: 12957
  Sorted by residual:
  angle pdb=" N   THR D 352 "
        pdb=" CA  THR D 352 "
        pdb=" C   THR D 352 "
      ideal   model   delta    sigma   weight residual
     111.03  121.20  -10.17 1.11e+00 8.12e-01 8.39e+01
  angle pdb=" N   ARG D 398 "
        pdb=" CA  ARG D 398 "
        pdb=" C   ARG D 398 "
      ideal   model   delta    sigma   weight residual
     113.41  102.54   10.87 1.22e+00 6.72e-01 7.95e+01
  angle pdb=" N   ILE D 439 "
        pdb=" CA  ILE D 439 "
        pdb=" C   ILE D 439 "
      ideal   model   delta    sigma   weight residual
     108.93   99.38    9.55 1.35e+00 5.49e-01 5.00e+01
  angle pdb=" CA  GLY D 460 "
        pdb=" C   GLY D 460 "
        pdb=" O   GLY D 460 "
      ideal   model   delta    sigma   weight residual
     122.22  117.63    4.59 6.50e-01 2.37e+00 4.98e+01
  angle pdb=" C   THR D 352 "
        pdb=" CA  THR D 352 "
        pdb=" CB  THR D 352 "
      ideal   model   delta    sigma   weight residual
     110.95  100.80   10.15 1.55e+00 4.16e-01 4.29e+01
  ... (remaining 12952 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.28: 4525
       35.28 -    70.56: 733
       70.56 -   105.84: 69
      105.84 -   141.12: 11
      141.12 -   176.40: 13
  Dihedral angle restraints: 5351
    sinusoidal: 4183
      harmonic: 1168
  Sorted by residual:
  dihedral pdb=" C5'   A C  93 "
           pdb=" C4'   A C  93 "
           pdb=" C3'   A C  93 "
           pdb=" O3'   A C  93 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   77.07   69.93     1      8.00e+00 1.56e-02 9.85e+01
  dihedral pdb=" O4'   C C  60 "
           pdb=" C1'   C C  60 "
           pdb=" N1    C C  60 "
           pdb=" C2    C C  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   31.04  168.96     1      1.50e+01 4.44e-03 8.45e+01
  dihedral pdb=" C4'   A C  93 "
           pdb=" C3'   A C  93 "
           pdb=" C2'   A C  93 "
           pdb=" C1'   A C  93 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   27.93  -62.93     1      8.00e+00 1.56e-02 8.17e+01
  ... (remaining 5348 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 1037
       0.081 -    0.163: 443
       0.163 -    0.244: 102
       0.244 -    0.325: 5
       0.325 -    0.406: 5
  Chirality restraints: 1592
  Sorted by residual:
  chirality pdb=" CA  LYS D  31 "
            pdb=" N   LYS D  31 "
            pdb=" C   LYS D  31 "
            pdb=" CB  LYS D  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.13e+00
  chirality pdb=" C3'  DT B 113 "
            pdb=" C4'  DT B 113 "
            pdb=" O3'  DT B 113 "
            pdb=" C2'  DT B 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.27   -0.39 2.00e-01 2.50e+01 3.85e+00
  chirality pdb=" CA  ASN D 382 "
            pdb=" N   ASN D 382 "
            pdb=" C   ASN D 382 "
            pdb=" CB  ASN D 382 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.75e+00
  ... (remaining 1589 not shown)

  Planarity restraints: 798
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC A  27 "    0.052 2.00e-02 2.50e+03   2.51e-02 1.42e+01
        pdb=" N1   DC A  27 "   -0.048 2.00e-02 2.50e+03
        pdb=" C2   DC A  27 "   -0.008 2.00e-02 2.50e+03
        pdb=" O2   DC A  27 "   -0.009 2.00e-02 2.50e+03
        pdb=" N3   DC A  27 "    0.005 2.00e-02 2.50e+03
        pdb=" C4   DC A  27 "    0.012 2.00e-02 2.50e+03
        pdb=" N4   DC A  27 "    0.014 2.00e-02 2.50e+03
        pdb=" C5   DC A  27 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6   DC A  27 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C  78 "    0.048 2.00e-02 2.50e+03   2.24e-02 1.38e+01
        pdb=" N9    A C  78 "   -0.053 2.00e-02 2.50e+03
        pdb=" C8    A C  78 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7    A C  78 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    A C  78 "    0.003 2.00e-02 2.50e+03
        pdb=" C6    A C  78 "    0.009 2.00e-02 2.50e+03
        pdb=" N6    A C  78 "    0.007 2.00e-02 2.50e+03
        pdb=" N1    A C  78 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    A C  78 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A C  78 "   -0.008 2.00e-02 2.50e+03
        pdb=" C4    A C  78 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG A   9 "    0.038 2.00e-02 2.50e+03   1.94e-02 1.13e+01
        pdb=" N9   DG A   9 "   -0.051 2.00e-02 2.50e+03
        pdb=" C8   DG A   9 "    0.002 2.00e-02 2.50e+03
        pdb=" N7   DG A   9 "    0.006 2.00e-02 2.50e+03
        pdb=" C5   DG A   9 "    0.008 2.00e-02 2.50e+03
        pdb=" C6   DG A   9 "    0.013 2.00e-02 2.50e+03
        pdb=" O6   DG A   9 "   -0.003 2.00e-02 2.50e+03
        pdb=" N1   DG A   9 "    0.002 2.00e-02 2.50e+03
        pdb=" C2   DG A   9 "    0.000 2.00e-02 2.50e+03
        pdb=" N2   DG A   9 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DG A   9 "   -0.009 2.00e-02 2.50e+03
        pdb=" C4   DG A   9 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 795 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2129
        2.80 -     3.33: 7862
        3.33 -     3.85: 17670
        3.85 -     4.38: 20559
        4.38 -     4.90: 26863
  Nonbonded interactions: 75083
  Sorted by model distance:
  nonbonded pdb=" OG  SER D   8 "
            pdb=" OG  SER D  10 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O2'   G C  95 "
            pdb=" N2    G C 131 "
     model   vdw
     2.309 3.120
  nonbonded pdb=" OD1 ASN D 154 "
            pdb=" O2'   U C 125 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" N3    C C 111 "
            pdb=" O6    G C 172 "
     model   vdw
     2.327 2.496
  nonbonded pdb=" O   ASN D 154 "
            pdb=" O2'   C C  98 "
     model   vdw
     2.352 3.040
  ... (remaining 75078 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=1.00 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:             1.290
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.590
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4489
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      :  0.009   0.074   8782  Z= 0.657
  Angle     :  1.320  10.875  12957  Z= 0.934
  Chirality :  0.090   0.406   1592
  Planarity :  0.005   0.071    798
  Dihedral  : 27.577 176.404   4599
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 32.18
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 12.09 %
    Favored  : 87.41 %
  Rotamer:
    Outliers :  7.20 %
    Allowed  : 17.00 %
    Favored  : 75.79 %
  Cbeta Deviations :  1.06 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.68 (0.29), residues: 397
  helix: -4.32 (0.23), residues: 113
  sheet: -3.35 (0.52), residues: 72
  loop : -3.66 (0.30), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D  86 
 TYR   0.011   0.002   TYR D 433 
 PHE   0.012   0.002   PHE D 196 
 TRP   0.004   0.001   TRP D 161 
 HIS   0.008   0.002   HIS D 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00949 ( 8782)
  covalent geometry    : angle       1.31985 (12957)
  hydrogen bonds       : bond        0.22740 (  304)
  hydrogen bonds       : angle      14.52390 (  680)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  175 ASN cc_start: 0.6017 (m-40) cc_final: 0.5698 (m-40)
REVERT: D  443 SER cc_start: 0.6737 (m) cc_final: 0.6077 (t)
REVERT: D  470 VAL cc_start: 0.5463 (OUTLIER) cc_final: 0.5218 (t)
  outliers start: 25
  outliers final: 3
  residues processed: 129
  average time/residue: 0.1379
  time to fit residues: 21.8332
Evaluate side-chains
  77 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  296 LEU
Chi-restraints excluded: chain D residue  394 VAL
Chi-restraints excluded: chain D residue  470 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
D  53 GLN
** D 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 373 HIS
D 376 GLN
D 428 HIS
D 462 ASN
D 465 GLN
D 487 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.126148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.091960 restraints weight = 14169.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 1.82
r_work: 0.3292 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6541
moved from start:          0.4898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.101   8782  Z= 0.299
  Angle     :  0.976  15.126  12957  Z= 0.498
  Chirality :  0.050   0.372   1592
  Planarity :  0.007   0.065    798
  Dihedral  : 27.163 179.565   3785
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 15.27 %
    Favored  : 78.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.28 (0.37), residues: 397
  helix: -1.71 (0.42), residues: 117
  sheet: -3.01 (0.54), residues: 68
  loop : -2.13 (0.38), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 131 
 TYR   0.020   0.003   TYR D 388 
 PHE   0.030   0.004   PHE D 318 
 TRP   0.004   0.001   TRP D 478 
 HIS   0.019   0.003   HIS D  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00649 ( 8782)
  covalent geometry    : angle       0.97630 (12957)
  hydrogen bonds       : bond        0.09667 (  304)
  hydrogen bonds       : angle       4.46111 (  680)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
REVERT: D  145 ILE cc_start: 0.5895 (OUTLIER) cc_final: 0.5639 (pt)
REVERT: D  148 LYS cc_start: 0.5853 (tttt) cc_final: 0.5280 (tptt)
REVERT: D  402 MET cc_start: 0.6085 (OUTLIER) cc_final: 0.5639 (mmm)
REVERT: D  436 MET cc_start: 0.7630 (mmm) cc_final: 0.7298 (mmm)
REVERT: D  461 ARG cc_start: 0.7849 (mmm160) cc_final: 0.7544 (mtp85)
REVERT: D  463 LYS cc_start: 0.8493 (mttm) cc_final: 0.8170 (mppt)
  outliers start: 21
  outliers final: 8
  residues processed: 93
  average time/residue: 0.0959
  time to fit residues: 11.9522
Evaluate side-chains
  63 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    6 VAL
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  341 LEU
Chi-restraints excluded: chain D residue  359 SER
Chi-restraints excluded: chain D residue  402 MET
Chi-restraints excluded: chain D residue  425 THR
Chi-restraints excluded: chain D residue  430 SER
Chi-restraints excluded: chain D residue  449 GLU
Chi-restraints excluded: chain D residue  494 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 46 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
D 194 ASN
D 300 ASN
D 376 GLN
** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.126770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.092421 restraints weight = 13954.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 1.75
r_work: 0.3302 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6965
moved from start:          0.7216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071   8782  Z= 0.233
  Angle     :  0.795  18.591  12957  Z= 0.413
  Chirality :  0.043   0.289   1592
  Planarity :  0.006   0.057    798
  Dihedral  : 26.442 178.464   3781
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 17.29 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.51 (0.38), residues: 397
  helix: -0.82 (0.44), residues: 118
  sheet: -2.14 (0.54), residues: 78
  loop : -1.95 (0.40), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D 113 
 TYR   0.017   0.002   TYR D   5 
 PHE   0.047   0.003   PHE D 329 
 TRP   0.008   0.003   TRP D 478 
 HIS   0.011   0.003   HIS D  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 8782)
  covalent geometry    : angle       0.79531 (12957)
  hydrogen bonds       : bond        0.06764 (  304)
  hydrogen bonds       : angle       4.11676 (  680)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.184 
Fit side-chains
REVERT: D   33 ARG cc_start: 0.6316 (ptm-80) cc_final: 0.5997 (ptm-80)
REVERT: D  183 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7374 (mt)
REVERT: D  402 MET cc_start: 0.7418 (tpt) cc_final: 0.6820 (mmm)
REVERT: D  461 ARG cc_start: 0.7943 (mmm160) cc_final: 0.7481 (ttm-80)
  outliers start: 13
  outliers final: 6
  residues processed: 84
  average time/residue: 0.0895
  time to fit residues: 10.2822
Evaluate side-chains
  56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain D residue   68 MET
Chi-restraints excluded: chain D residue  183 ILE
Chi-restraints excluded: chain D residue  394 VAL
Chi-restraints excluded: chain D residue  445 LEU
Chi-restraints excluded: chain D residue  454 THR
Chi-restraints excluded: chain D residue  494 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 53 optimal weight:    7.9990
   chunk 57 optimal weight:    9.9990
   chunk 2 optimal weight:    0.0970
   chunk 10 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   overall best weight:    1.1780

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

Flipped N/Q/H residues before XYZ refinement:
D 194 ASN
D 369 GLN
D 404 GLN
D 492 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.127848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.093644 restraints weight = 14531.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 1.68
r_work: 0.3402 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3278 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.9700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.101   8782  Z= 0.237
  Angle     :  0.811  11.447  12957  Z= 0.416
  Chirality :  0.043   0.278   1592
  Planarity :  0.007   0.073    798
  Dihedral  : 26.313 174.434   3780
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 17.87 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.94 (0.40), residues: 397
  helix: -0.49 (0.43), residues: 120
  sheet: -2.00 (0.58), residues: 73
  loop : -1.44 (0.42), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG D 372 
 TYR   0.012   0.002   TYR D 340 
 PHE   0.029   0.003   PHE D 198 
 TRP   0.006   0.002   TRP D 478 
 HIS   0.007   0.002   HIS D 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 ( 8782)
  covalent geometry    : angle       0.81082 (12957)
  hydrogen bonds       : bond        0.07262 (  304)
  hydrogen bonds       : angle       3.92307 (  680)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
REVERT: D  167 ASN cc_start: 0.8221 (t0) cc_final: 0.7978 (t0)
REVERT: D  183 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8275 (mt)
  outliers start: 13
  outliers final: 6
  residues processed: 60
  average time/residue: 0.0863
  time to fit residues: 7.3008
Evaluate side-chains
  48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   89 ASP
Chi-restraints excluded: chain D residue  183 ILE
Chi-restraints excluded: chain D residue  193 LEU
Chi-restraints excluded: chain D residue  371 ARG
Chi-restraints excluded: chain D residue  430 SER
Chi-restraints excluded: chain D residue  449 GLU
Chi-restraints excluded: chain D residue  491 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 53 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   chunk 44 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 8 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 46 optimal weight:    6.9990
   overall best weight:    2.1384

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

Flipped N/Q/H residues before XYZ refinement:
** D 175 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 = 0.3966 r_free = 0.3966 target = 0.122607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.087464 restraints weight = 14316.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 1.69
r_work: 0.3298 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3177 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          1.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   8782  Z= 0.297
  Angle     :  0.810   9.594  12957  Z= 0.425
  Chirality :  0.045   0.334   1592
  Planarity :  0.006   0.042    798
  Dihedral  : 26.237 178.687   3780
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 16.71 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.93 (0.39), residues: 397
  helix: -0.40 (0.45), residues: 119
  sheet: -1.84 (0.59), residues: 73
  loop : -1.56 (0.40), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 116 
 TYR   0.021   0.002   TYR D 340 
 PHE   0.025   0.003   PHE D 198 
 TRP   0.007   0.002   TRP D 161 
 HIS   0.005   0.002   HIS D 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00628 ( 8782)
  covalent geometry    : angle       0.80989 (12957)
  hydrogen bonds       : bond        0.06774 (  304)
  hydrogen bonds       : angle       4.12621 (  680)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 44
  time to evaluate  : 0.177 
Fit side-chains
REVERT: D    1 MET cc_start: 0.8537 (mmp) cc_final: 0.8241 (mmm)
REVERT: D   37 ARG cc_start: 0.7672 (ttp80) cc_final: 0.7046 (ttm110)
REVERT: D  371 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.7796 (mtp85)
REVERT: D  393 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8189 (pt)
REVERT: D  440 MET cc_start: 0.8706 (mmm) cc_final: 0.8131 (mmm)
  outliers start: 20
  outliers final: 11
  residues processed: 60
  average time/residue: 0.0908
  time to fit residues: 7.4992
Evaluate side-chains
  48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 35
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain D residue   89 ASP
Chi-restraints excluded: chain D residue  141 THR
Chi-restraints excluded: chain D residue  183 ILE
Chi-restraints excluded: chain D residue  193 LEU
Chi-restraints excluded: chain D residue  310 LEU
Chi-restraints excluded: chain D residue  371 ARG
Chi-restraints excluded: chain D residue  393 LEU
Chi-restraints excluded: chain D residue  394 VAL
Chi-restraints excluded: chain D residue  425 THR
Chi-restraints excluded: chain D residue  449 GLU
Chi-restraints excluded: chain D residue  491 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 50 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 8 optimal weight:    0.1980
   chunk 49 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0970
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.125390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.090964 restraints weight = 14253.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 1.61
r_work: 0.3354 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3230 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          1.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8782  Z= 0.169
  Angle     :  0.676  12.665  12957  Z= 0.357
  Chirality :  0.039   0.313   1592
  Planarity :  0.004   0.036    798
  Dihedral  : 26.003 175.497   3780
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 19.88 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.26 (0.41), residues: 397
  helix:  0.33 (0.48), residues: 118
  sheet: -1.24 (0.70), residues: 60
  loop : -1.37 (0.40), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 385 
 TYR   0.020   0.002   TYR D 340 
 PHE   0.022   0.002   PHE D 318 
 TRP   0.004   0.001   TRP D 161 
 HIS   0.003   0.001   HIS D  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8782)
  covalent geometry    : angle       0.67564 (12957)
  hydrogen bonds       : bond        0.05254 (  304)
  hydrogen bonds       : angle       3.59569 (  680)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.184 
Fit side-chains
REVERT: D   37 ARG cc_start: 0.7472 (ttp80) cc_final: 0.6992 (ttm110)
REVERT: D   72 THR cc_start: 0.8294 (p) cc_final: 0.8020 (p)
REVERT: D  183 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8557 (mt)
REVERT: D  333 HIS cc_start: 0.7426 (m90) cc_final: 0.7166 (m90)
REVERT: D  403 ASP cc_start: 0.7842 (t0) cc_final: 0.7449 (t0)
  outliers start: 8
  outliers final: 5
  residues processed: 48
  average time/residue: 0.0888
  time to fit residues: 5.9530
Evaluate side-chains
  45 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  140 ILE
Chi-restraints excluded: chain D residue  183 ILE
Chi-restraints excluded: chain D residue  303 ILE
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  449 GLU
Chi-restraints excluded: chain D residue  491 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0030
   chunk 16 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 46 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.8592

-------------------------------------------------------------------------------
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 = 0.4023 r_free = 0.4023 target = 0.126383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.092158 restraints weight = 14293.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 1.60
r_work: 0.3380 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3258 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          1.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8782  Z= 0.164
  Angle     :  0.632  10.653  12957  Z= 0.338
  Chirality :  0.037   0.283   1592
  Planarity :  0.004   0.040    798
  Dihedral  : 25.853 176.638   3780
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 19.60 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.42), residues: 397
  helix:  0.84 (0.50), residues: 118
  sheet: -1.03 (0.69), residues: 61
  loop : -1.04 (0.41), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 330 
 TYR   0.019   0.001   TYR D 340 
 PHE   0.009   0.002   PHE D 198 
 TRP   0.003   0.001   TRP D 161 
 HIS   0.005   0.001   HIS D 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 8782)
  covalent geometry    : angle       0.63231 (12957)
  hydrogen bonds       : bond        0.05135 (  304)
  hydrogen bonds       : angle       3.53809 (  680)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.173 
Fit side-chains
REVERT: D   37 ARG cc_start: 0.7378 (ttp80) cc_final: 0.7028 (ttm110)
REVERT: D  333 HIS cc_start: 0.7601 (m90) cc_final: 0.7351 (m90)
REVERT: D  402 MET cc_start: 0.8502 (mmm) cc_final: 0.8273 (mmt)
REVERT: D  403 ASP cc_start: 0.7769 (t0) cc_final: 0.7356 (t0)
  outliers start: 8
  outliers final: 5
  residues processed: 50
  average time/residue: 0.0836
  time to fit residues: 5.7895
Evaluate side-chains
  43 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  140 ILE
Chi-restraints excluded: chain D residue  426 VAL
Chi-restraints excluded: chain D residue  430 SER
Chi-restraints excluded: chain D residue  449 GLU
Chi-restraints excluded: chain D residue  493 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
D 130 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.122051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.087140 restraints weight = 14129.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.64
r_work: 0.3292 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          1.3726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8782  Z= 0.225
  Angle     :  0.718  13.650  12957  Z= 0.374
  Chirality :  0.040   0.299   1592
  Planarity :  0.005   0.039    798
  Dihedral  : 25.853 176.066   3780
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 19.60 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.82 (0.41), residues: 397
  helix:  0.56 (0.48), residues: 117
  sheet: -0.85 (0.64), residues: 69
  loop : -1.04 (0.41), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 385 
 TYR   0.031   0.002   TYR D 340 
 PHE   0.011   0.002   PHE D 318 
 TRP   0.005   0.002   TRP D 478 
 HIS   0.005   0.001   HIS D 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 ( 8782)
  covalent geometry    : angle       0.71791 (12957)
  hydrogen bonds       : bond        0.06062 (  304)
  hydrogen bonds       : angle       3.60908 (  680)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.175 
Fit side-chains
REVERT: D   37 ARG cc_start: 0.7534 (ttp80) cc_final: 0.6953 (ttm110)
REVERT: D  402 MET cc_start: 0.8529 (mmm) cc_final: 0.8308 (mmt)
REVERT: D  403 ASP cc_start: 0.7845 (t0) cc_final: 0.7415 (t0)
  outliers start: 9
  outliers final: 7
  residues processed: 46
  average time/residue: 0.0928
  time to fit residues: 5.8226
Evaluate side-chains
  40 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  140 ILE
Chi-restraints excluded: chain D residue  141 THR
Chi-restraints excluded: chain D residue  177 VAL
Chi-restraints excluded: chain D residue  426 VAL
Chi-restraints excluded: chain D residue  430 SER
Chi-restraints excluded: chain D residue  449 GLU
Chi-restraints excluded: chain D residue  493 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 29 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 40 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 48 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
D  82 GLN
D  99 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.124365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.089656 restraints weight = 14197.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 1.60
r_work: 0.3333 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          1.4038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8782  Z= 0.183
  Angle     :  0.641  10.066  12957  Z= 0.343
  Chirality :  0.038   0.275   1592
  Planarity :  0.004   0.037    798
  Dihedral  : 25.820 178.632   3780
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 19.31 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.42), residues: 397
  helix:  0.87 (0.49), residues: 117
  sheet: -0.26 (0.75), residues: 59
  loop : -0.96 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 330 
 TYR   0.024   0.001   TYR D 340 
 PHE   0.019   0.002   PHE D 329 
 TRP   0.004   0.001   TRP D 161 
 HIS   0.004   0.001   HIS D 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 8782)
  covalent geometry    : angle       0.64147 (12957)
  hydrogen bonds       : bond        0.05374 (  304)
  hydrogen bonds       : angle       3.46399 (  680)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 36
  time to evaluate  : 0.155 
Fit side-chains
REVERT: D  179 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8375 (ttmm)
REVERT: D  369 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8379 (mm-40)
REVERT: D  402 MET cc_start: 0.8474 (mmm) cc_final: 0.8253 (mmt)
REVERT: D  403 ASP cc_start: 0.7813 (t0) cc_final: 0.7439 (t0)
REVERT: D  440 MET cc_start: 0.8661 (mmm) cc_final: 0.8325 (mmm)
  outliers start: 10
  outliers final: 5
  residues processed: 44
  average time/residue: 0.1015
  time to fit residues: 5.9414
Evaluate side-chains
  40 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  140 ILE
Chi-restraints excluded: chain D residue  141 THR
Chi-restraints excluded: chain D residue  179 LYS
Chi-restraints excluded: chain D residue  369 GLN
Chi-restraints excluded: chain D residue  426 VAL
Chi-restraints excluded: chain D residue  449 GLU
Chi-restraints excluded: chain D residue  493 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 12 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   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  82 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.123223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.088152 restraints weight = 14166.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 1.62
r_work: 0.3293 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          1.4313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8782  Z= 0.192
  Angle     :  0.658   9.823  12957  Z= 0.350
  Chirality :  0.038   0.273   1592
  Planarity :  0.004   0.036    798
  Dihedral  : 25.812 178.628   3780
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 19.02 %
    Favored  : 78.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.41), residues: 397
  helix:  0.61 (0.47), residues: 117
  sheet: -0.20 (0.75), residues: 59
  loop : -0.86 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 110 
 TYR   0.007   0.001   TYR D 340 
 PHE   0.015   0.002   PHE D 329 
 TRP   0.003   0.001   TRP D 478 
 HIS   0.007   0.001   HIS D 333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 8782)
  covalent geometry    : angle       0.65816 (12957)
  hydrogen bonds       : bond        0.05650 (  304)
  hydrogen bonds       : angle       3.48059 (  680)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 0.172 
Fit side-chains
REVERT: D   68 MET cc_start: 0.8112 (mpp) cc_final: 0.7338 (mpp)
REVERT: D  179 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8283 (ttmm)
REVERT: D  402 MET cc_start: 0.8479 (mmm) cc_final: 0.8253 (mmt)
REVERT: D  403 ASP cc_start: 0.7856 (t0) cc_final: 0.7461 (t0)
REVERT: D  440 MET cc_start: 0.8656 (mmm) cc_final: 0.8332 (mmm)
  outliers start: 8
  outliers final: 6
  residues processed: 43
  average time/residue: 0.1043
  time to fit residues: 5.9903
Evaluate side-chains
  41 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 34
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  140 ILE
Chi-restraints excluded: chain D residue  141 THR
Chi-restraints excluded: chain D residue  179 LYS
Chi-restraints excluded: chain D residue  426 VAL
Chi-restraints excluded: chain D residue  430 SER
Chi-restraints excluded: chain D residue  449 GLU
Chi-restraints excluded: chain D residue  493 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 12 optimal weight:    0.0670
   chunk 8 optimal weight:    0.6980
   chunk 53 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 22 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 40 optimal weight:    6.9990
   chunk 43 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   overall best weight:    0.6722

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

Flipped N/Q/H residues before XYZ refinement:
D 369 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.125895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.091244 restraints weight = 13982.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 1.61
r_work: 0.3365 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          1.4444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8782  Z= 0.149
  Angle     :  0.637  12.874  12957  Z= 0.339
  Chirality :  0.036   0.254   1592
  Planarity :  0.004   0.038    798
  Dihedral  : 25.751 179.164   3780
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 18.73 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.42), residues: 397
  helix:  0.83 (0.48), residues: 118
  sheet: -0.41 (0.61), residues: 76
  loop : -0.73 (0.43), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  37 
 TYR   0.009   0.001   TYR D 340 
 PHE   0.010   0.002   PHE D 329 
 TRP   0.003   0.001   TRP D 161 
 HIS   0.003   0.001   HIS D 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8782)
  covalent geometry    : angle       0.63702 (12957)
  hydrogen bonds       : bond        0.05176 (  304)
  hydrogen bonds       : angle       3.41828 (  680)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2838.46 seconds
wall clock time: 48 minutes 56.55 seconds (2936.55 seconds total)