Starting phenix.real_space_refine
on Tue Mar  3 18:53:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7utn_26782/03_2026/7utn_26782.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7utn_26782/03_2026/7utn_26782.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7utn_26782/03_2026/7utn_26782.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7utn_26782/03_2026/7utn_26782.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7utn_26782/03_2026/7utn_26782.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7utn_26782/03_2026/7utn_26782.cif"
  }
  resolution = 2.74
  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=   0.026
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     228      5.49       5
     S      21      5.16       5
     C    4183      2.51       5
     N    1470      2.21       5
     O    2101      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 8003
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "D"
      Number of atoms: 3174
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 397, 3174
          Classifications: {'peptide': 397}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 378}
          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': 14, 'rna2p_pyr': 12, 'rna3p_pur': 90, 'rna3p_pyr': 68}
          Link IDs: {'rna2p': 25, 'rna3p': 158}
          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: 313
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 313
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
  Time building chain proxies: 2.13, per 1000 atoms: 0.27
  Number of scatterers: 8003
  At special positions: 0
  Unit cell: (90.95, 105.93, 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     228     15.00
     O    2101      8.00
     N    1470      7.00
     C    4183      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: 0.75
  Conformation dependent library (CDL) restraints added in 131.8 milliseconds
  

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  744

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 6 sheets defined
      30.0% alpha, 20.4% beta
      76 base pairs and 137 stacking pairs defined.
    Time for finding SS restraints: 1.22
  Creating SS restraints...
    Processing helix  chain 'D' and resid 21 through 29
    Processing helix  chain 'D' and resid 88 through 109
      removed outlier: 4.313A  pdb=" N   LYS D  92 " --> pdb=" O   LYS D  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 109 through 121
    Processing helix  chain 'D' and resid 163 through 184
      removed outlier: 3.662A  pdb=" N   ILE D 183 " --> pdb=" O   LYS D 179 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 314
      Proline residue:  D 304  - end of helix
    Processing helix  chain 'D' and resid 323 through 334
    Processing helix  chain 'D' and resid 340 through 348
      removed outlier: 4.588A  pdb=" N   TYR D 344 " --> pdb=" O   TYR D 340 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 408 through 416
    Processing helix  chain 'D' and resid 417 through 422
    Processing sheet with id=AA1, first strand: chain 'D' and resid 5 through 7
      removed outlier: 6.264A  pdb=" N   TYR D   5 " --> pdb=" O   ILE D  42 " (cutoff:3.500A)
      removed outlier: 7.458A  pdb=" N   LEU D  44 " --> pdb=" O   TYR D   5 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   ILE D   7 " --> pdb=" O   LEU D  44 " (cutoff:3.500A)
      removed outlier: 6.402A  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: 6.231A  pdb=" N   VAL D 189 " --> pdb=" O   CYS D 319 " (cutoff:3.500A)
      removed outlier: 7.629A  pdb=" N   THR D 321 " --> pdb=" O   VAL D 189 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   LEU D 191 " --> pdb=" O   THR D 321 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   LEU D  57 " --> pdb=" O   VAL D 190 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   GLU D 192 " --> pdb=" O   LEU D  57 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   ILE D  59 " --> pdb=" O   GLU D 192 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   PHE D  79 " --> pdb=" O   VAL D  70 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLN D 369 " --> pdb=" O   GLU D  84 " (cutoff:3.500A)
      removed outlier: 4.864A  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
      removed outlier: 6.559A  pdb=" N   GLN D 432 " --> pdb=" O   HIS D 379 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 392 through 395
      removed outlier: 6.610A  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: 4.836A  pdb=" N   VAL D 466 " --> pdb=" O   GLY D 460 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   GLY D 460 " --> pdb=" O   VAL D 466 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   TYR D 468 " --> pdb=" O   SER D 458 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   SER D 458 " --> pdb=" O   TYR D 468 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   VAL D 470 " --> pdb=" O   SER D 456 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   ILE D 444 " --> pdb=" O   LEU D 485 " (cutoff:3.500A)

    118 hydrogen bonds defined for protein.
    330 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      196 hydrogen bonds
      364 hydrogen bond angles
      0 basepair planarities
      76 basepair parallelities
      137 stacking parallelities
  Total time for adding SS restraints: 1.67

  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:
        1.21 -     1.33: 1144
        1.33 -     1.45: 3372
        1.45 -     1.56: 3635
        1.56 -     1.68: 451
        1.68 -     1.80: 33
  Bond restraints: 8635
  Sorted by residual:
  bond pdb=" O3'   U C 205 "
       pdb=" P     U C 206 "
    ideal  model  delta    sigma   weight residual
    1.607  1.572  0.035 1.50e-02 4.44e+03 5.50e+00
  bond pdb=" N   ASN D  65 "
       pdb=" CA  ASN D  65 "
    ideal  model  delta    sigma   weight residual
    1.466  1.443  0.023 1.36e-02 5.41e+03 2.93e+00
  bond pdb=" CA  ARG D 151 "
       pdb=" CB  ARG D 151 "
    ideal  model  delta    sigma   weight residual
    1.527  1.497  0.030 1.75e-02 3.27e+03 2.93e+00
  bond pdb=" SD  MET D  68 "
       pdb=" CE  MET D  68 "
    ideal  model  delta    sigma   weight residual
    1.791  1.748  0.043 2.50e-02 1.60e+03 2.92e+00
  bond pdb=" N   ARG D 330 "
       pdb=" CA  ARG D 330 "
    ideal  model  delta    sigma   weight residual
    1.459  1.441  0.018 1.17e-02 7.31e+03 2.43e+00
  ... (remaining 8630 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 12339
        1.72 -     3.43: 338
        3.43 -     5.15: 54
        5.15 -     6.87: 4
        6.87 -     8.58: 1
  Bond angle restraints: 12736
  Sorted by residual:
  angle pdb=" C4'   U C 206 "
        pdb=" C3'   U C 206 "
        pdb=" O3'   U C 206 "
      ideal   model   delta    sigma   weight residual
     109.40  117.98   -8.58 1.50e+00 4.44e-01 3.27e+01
  angle pdb=" C3'   A C 128 "
        pdb=" C2'   A C 128 "
        pdb=" C1'   A C 128 "
      ideal   model   delta    sigma   weight residual
     101.50  105.10   -3.60 1.00e+00 1.00e+00 1.30e+01
  angle pdb=" C4'   A C 128 "
        pdb=" C3'   A C 128 "
        pdb=" O3'   A C 128 "
      ideal   model   delta    sigma   weight residual
     109.40  114.76   -5.36 1.50e+00 4.44e-01 1.27e+01
  angle pdb=" C3'   A C  78 "
        pdb=" C2'   A C  78 "
        pdb=" C1'   A C  78 "
      ideal   model   delta    sigma   weight residual
     101.30  104.71   -3.41 1.00e+00 1.00e+00 1.16e+01
  angle pdb=" C2'   A C  78 "
        pdb=" C1'   A C  78 "
        pdb=" N9    A C  78 "
      ideal   model   delta    sigma   weight residual
     112.00  106.96    5.04 1.50e+00 4.44e-01 1.13e+01
  ... (remaining 12731 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.57: 4683
       35.57 -    71.15: 533
       71.15 -   106.72: 52
      106.72 -   142.29: 4
      142.29 -   177.87: 10
  Dihedral angle restraints: 5282
    sinusoidal: 4127
      harmonic: 1155
  Sorted by residual:
  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   36.86  163.14     1      1.50e+01 4.44e-03 8.35e+01
  dihedral pdb=" O4'   U C 204 "
           pdb=" C1'   U C 204 "
           pdb=" N1    U C 204 "
           pdb=" C2    U C 204 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   46.30  153.70     1      1.50e+01 4.44e-03 8.09e+01
  dihedral pdb=" O4'   U C 180 "
           pdb=" C1'   U C 180 "
           pdb=" N1    U C 180 "
           pdb=" C2    U C 180 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -28.49 -131.51     1      1.50e+01 4.44e-03 7.09e+01
  ... (remaining 5279 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 1455
       0.072 -    0.144: 101
       0.144 -    0.216: 7
       0.216 -    0.288: 3
       0.288 -    0.361: 1
  Chirality restraints: 1567
  Sorted by residual:
  chirality pdb=" C3'   A C 128 "
            pdb=" C4'   A C 128 "
            pdb=" O3'   A C 128 "
            pdb=" C2'   A C 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.38   -0.36 2.00e-01 2.50e+01 3.25e+00
  chirality pdb=" C2'   A C  78 "
            pdb=" C3'   A C  78 "
            pdb=" O2'   A C  78 "
            pdb=" C1'   A C  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.48   -0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" C1'   G C 121 "
            pdb=" O4'   G C 121 "
            pdb=" C2'   G C 121 "
            pdb=" N9    G C 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.22    0.23 2.00e-01 2.50e+01 1.38e+00
  ... (remaining 1564 not shown)

  Planarity restraints: 787
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C  78 "   -0.042 2.00e-02 2.50e+03   2.12e-02 1.24e+01
        pdb=" N9    A C  78 "    0.055 2.00e-02 2.50e+03
        pdb=" C8    A C  78 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    A C  78 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5    A C  78 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6    A C  78 "   -0.005 2.00e-02 2.50e+03
        pdb=" N6    A C  78 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    A C  78 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A C  78 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    A C  78 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    A C  78 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C  91 "   -0.034 2.00e-02 2.50e+03   1.45e-02 6.27e+00
        pdb=" N9    G C  91 "    0.034 2.00e-02 2.50e+03
        pdb=" C8    G C  91 "    0.004 2.00e-02 2.50e+03
        pdb=" N7    G C  91 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G C  91 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    G C  91 "   -0.003 2.00e-02 2.50e+03
        pdb=" O6    G C  91 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1    G C  91 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    G C  91 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G C  91 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G C  91 "    0.006 2.00e-02 2.50e+03
        pdb=" C4    G C  91 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 163 "   -0.037 5.00e-02 4.00e+02   5.61e-02 5.04e+00
        pdb=" N   PRO D 164 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO D 164 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO D 164 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 784 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 226
        2.64 -     3.21: 6504
        3.21 -     3.77: 15156
        3.77 -     4.34: 20706
        4.34 -     4.90: 28300
  Nonbonded interactions: 70892
  Sorted by model distance:
  nonbonded pdb=" O2'   A C  78 "
            pdb=" O4'   G C  79 "
     model   vdw
     2.080 3.040
  nonbonded pdb=" O4    U C  30 "
            pdb=" N6    A C  46 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" NH1 ARG D 115 "
            pdb=" OP2   C C  58 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" OH  TYR D  46 "
            pdb=" OP1   U C 206 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OD1 ASN D 487 "
            pdb=" N   ASN D 488 "
     model   vdw
     2.321 3.120
  ... (remaining 70887 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:             1.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.140
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
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      :  0.007   0.043   8635  Z= 0.333
  Angle     :  0.679   8.584  12736  Z= 0.394
  Chirality :  0.041   0.361   1567
  Planarity :  0.004   0.056    787
  Dihedral  : 23.532 177.868   4538
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  0.01 (0.40), residues: 393
  helix:  1.09 (0.47), residues: 117
  sheet: -0.44 (0.62), residues: 63
  loop : -0.40 (0.39), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 486 
 TYR   0.010   0.001   TYR D   5 
 PHE   0.010   0.002   PHE D 453 
 TRP   0.012   0.002   TRP D 161 
 HIS   0.003   0.001   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00674 ( 8635)
  covalent geometry    : angle       0.67924 (12736)
  hydrogen bonds       : bond        0.09493 (  314)
  hydrogen bonds       : angle       5.43414 (  694)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.162 
Fit side-chains
REVERT: D  102 MET cc_start: 0.8633 (mmt) cc_final: 0.8320 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.8613
  time to fit residues: 26.9676
Evaluate side-chains
  22 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 56 optimal weight:   10.0000
   chunk 26 optimal weight:    0.1980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** D  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.084761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.059782 restraints weight = 16873.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.2822 rms_B_bonded: 1.45
r_work: 0.2705 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2600 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.0799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8635  Z= 0.171
  Angle     :  0.589   6.717  12736  Z= 0.320
  Chirality :  0.036   0.287   1567
  Planarity :  0.005   0.056    787
  Dihedral  : 24.395 176.985   3725
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  4.65 %
    Favored  : 94.77 %
  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:  0.56 (0.40), residues: 393
  helix:  1.76 (0.46), residues: 118
  sheet: -0.09 (0.64), residues: 63
  loop : -0.23 (0.39), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 363 
 TYR   0.013   0.001   TYR D 327 
 PHE   0.007   0.001   PHE D 453 
 TRP   0.007   0.001   TRP D 161 
 HIS   0.004   0.001   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 8635)
  covalent geometry    : angle       0.58890 (12736)
  hydrogen bonds       : bond        0.04029 (  314)
  hydrogen bonds       : angle       3.58000 (  694)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 26
  time to evaluate  : 0.177 
Fit side-chains
REVERT: D  102 MET cc_start: 0.9169 (mmt) cc_final: 0.8909 (mmt)
  outliers start: 2
  outliers final: 2
  residues processed: 26
  average time/residue: 0.7698
  time to fit residues: 21.0028
Evaluate side-chains
  23 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 21
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   68 MET
Chi-restraints excluded: chain D residue  361 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 15 optimal weight:    0.2980
   chunk 1 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    2.2186

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

Flipped N/Q/H residues before XYZ refinement:
** D  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.082587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.057419 restraints weight = 16767.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.2767 rms_B_bonded: 1.47
r_work: 0.2649 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2544 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.0819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068   8635  Z= 0.309
  Angle     :  0.641   6.540  12736  Z= 0.347
  Chirality :  0.040   0.353   1567
  Planarity :  0.005   0.061    787
  Dihedral  : 24.388 177.298   3725
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  6.10 %
    Favored  : 93.31 %
  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:  0.56 (0.40), residues: 393
  helix:  1.78 (0.46), residues: 119
  sheet:  0.05 (0.63), residues: 70
  loop : -0.31 (0.40), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 363 
 TYR   0.023   0.002   TYR D 327 
 PHE   0.009   0.001   PHE D 453 
 TRP   0.010   0.001   TRP D 161 
 HIS   0.004   0.001   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00636 ( 8635)
  covalent geometry    : angle       0.64063 (12736)
  hydrogen bonds       : bond        0.04543 (  314)
  hydrogen bonds       : angle       3.53260 (  694)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.187 
Fit side-chains
REVERT: D  102 MET cc_start: 0.9159 (mmt) cc_final: 0.8879 (mmt)
  outliers start: 2
  outliers final: 2
  residues processed: 23
  average time/residue: 0.8700
  time to fit residues: 20.9480
Evaluate side-chains
  23 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 21
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   68 MET
Chi-restraints excluded: chain D residue  361 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 1 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** D  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 492 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.085355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.060391 restraints weight = 17062.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.2833 rms_B_bonded: 1.43
r_work: 0.2717 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2613 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8635  Z= 0.135
  Angle     :  0.580   7.584  12736  Z= 0.313
  Chirality :  0.035   0.268   1567
  Planarity :  0.005   0.055    787
  Dihedral  : 24.379 177.136   3725
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  7.27 %
    Favored  : 91.57 %
  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:  0.81 (0.41), residues: 393
  helix:  2.00 (0.46), residues: 119
  sheet:  0.13 (0.64), residues: 70
  loop : -0.14 (0.41), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 363 
 TYR   0.008   0.001   TYR D 484 
 PHE   0.006   0.001   PHE D 453 
 TRP   0.007   0.001   TRP D 161 
 HIS   0.006   0.001   HIS D 333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 8635)
  covalent geometry    : angle       0.57989 (12736)
  hydrogen bonds       : bond        0.03808 (  314)
  hydrogen bonds       : angle       3.33454 (  694)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.134 
Fit side-chains
REVERT: D   33 ARG cc_start: 0.7273 (ttp80) cc_final: 0.7039 (ttp80)
REVERT: D   73 GLU cc_start: 0.8186 (mp0) cc_final: 0.7843 (mp0)
REVERT: D  102 MET cc_start: 0.9197 (mmt) cc_final: 0.8940 (mmt)
REVERT: D  355 LYS cc_start: 0.8704 (mmpt) cc_final: 0.8406 (mtmp)
  outliers start: 4
  outliers final: 2
  residues processed: 28
  average time/residue: 0.7254
  time to fit residues: 21.3765
Evaluate side-chains
  24 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   68 MET
Chi-restraints excluded: chain D residue  361 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0470
   chunk 28 optimal weight:    6.9990
   chunk 46 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   overall best weight:    2.4086

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

Flipped N/Q/H residues before XYZ refinement:
** D  87 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 = 0.3267 r_free = 0.3267 target = 0.082466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.057234 restraints weight = 16921.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.2760 rms_B_bonded: 1.49
r_work: 0.2642 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2538 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.0982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.067   8635  Z= 0.331
  Angle     :  0.649   6.634  12736  Z= 0.350
  Chirality :  0.041   0.358   1567
  Planarity :  0.005   0.059    787
  Dihedral  : 24.305 177.197   3725
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  8.72 %
    Favored  : 90.41 %
  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:  0.73 (0.41), residues: 393
  helix:  1.93 (0.46), residues: 119
  sheet:  0.05 (0.64), residues: 70
  loop : -0.17 (0.40), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 363 
 TYR   0.010   0.001   TYR D   5 
 PHE   0.008   0.001   PHE D 453 
 TRP   0.008   0.001   TRP D 161 
 HIS   0.004   0.001   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00683 ( 8635)
  covalent geometry    : angle       0.64860 (12736)
  hydrogen bonds       : bond        0.04632 (  314)
  hydrogen bonds       : angle       3.45824 (  694)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.148 
Fit side-chains
REVERT: D   33 ARG cc_start: 0.7216 (ttp80) cc_final: 0.6989 (ttp80)
REVERT: D   73 GLU cc_start: 0.8245 (mp0) cc_final: 0.7850 (mp0)
  outliers start: 3
  outliers final: 2
  residues processed: 25
  average time/residue: 0.9006
  time to fit residues: 23.4687
Evaluate side-chains
  24 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   68 MET
Chi-restraints excluded: chain D residue  361 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** D  87 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 = 0.3303 r_free = 0.3303 target = 0.084319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.059119 restraints weight = 16811.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.2808 rms_B_bonded: 1.46
r_work: 0.2689 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2584 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.1139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8635  Z= 0.182
  Angle     :  0.588   6.706  12736  Z= 0.318
  Chirality :  0.037   0.333   1567
  Planarity :  0.004   0.055    787
  Dihedral  : 24.286 177.065   3725
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  8.72 %
    Favored  : 89.83 %
  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:  0.89 (0.41), residues: 393
  helix:  2.09 (0.46), residues: 119
  sheet:  0.11 (0.65), residues: 70
  loop : -0.08 (0.41), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 363 
 TYR   0.008   0.001   TYR D   5 
 PHE   0.007   0.001   PHE D 453 
 TRP   0.008   0.001   TRP D 161 
 HIS   0.003   0.001   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 8635)
  covalent geometry    : angle       0.58803 (12736)
  hydrogen bonds       : bond        0.04020 (  314)
  hydrogen bonds       : angle       3.34523 (  694)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 26
  time to evaluate  : 0.192 
Fit side-chains
REVERT: D   33 ARG cc_start: 0.7196 (ttp80) cc_final: 0.6958 (ttp80)
REVERT: D   37 ARG cc_start: 0.8424 (ttp80) cc_final: 0.7827 (ttp-110)
REVERT: D   73 GLU cc_start: 0.8269 (mp0) cc_final: 0.7862 (mp0)
  outliers start: 5
  outliers final: 2
  residues processed: 27
  average time/residue: 0.8042
  time to fit residues: 22.7847
Evaluate side-chains
  25 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   68 MET
Chi-restraints excluded: chain D residue  361 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0570
   chunk 17 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 38 optimal weight:    0.1980
   overall best weight:    0.8302

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

Flipped N/Q/H residues before XYZ refinement:
** D  87 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 = 0.3337 r_free = 0.3337 target = 0.086181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.061216 restraints weight = 16931.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 1.43
r_work: 0.2739 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2636 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.1480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8635  Z= 0.148
  Angle     :  0.550   7.328  12736  Z= 0.297
  Chirality :  0.034   0.274   1567
  Planarity :  0.004   0.056    787
  Dihedral  : 24.142 177.025   3725
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  9.59 %
    Favored  : 89.24 %
  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:  1.00 (0.42), residues: 393
  helix:  2.16 (0.46), residues: 121
  sheet:  0.28 (0.72), residues: 59
  loop : -0.05 (0.41), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 363 
 TYR   0.018   0.001   TYR D 327 
 PHE   0.010   0.001   PHE D 329 
 TRP   0.006   0.001   TRP D 161 
 HIS   0.003   0.001   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 8635)
  covalent geometry    : angle       0.54951 (12736)
  hydrogen bonds       : bond        0.03847 (  314)
  hydrogen bonds       : angle       3.19675 (  694)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 27
  time to evaluate  : 0.184 
Fit side-chains
REVERT: D   37 ARG cc_start: 0.8495 (ttp80) cc_final: 0.7917 (ttp-110)
REVERT: D  392 LYS cc_start: 0.8630 (mptt) cc_final: 0.8405 (mmtp)
  outliers start: 4
  outliers final: 1
  residues processed: 29
  average time/residue: 0.6774
  time to fit residues: 20.7521
Evaluate side-chains
  25 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   68 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0970
   chunk 22 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** D  87 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 = 0.3323 r_free = 0.3323 target = 0.085442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.060387 restraints weight = 16870.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.2837 rms_B_bonded: 1.45
r_work: 0.2718 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2612 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8635  Z= 0.179
  Angle     :  0.561   6.777  12736  Z= 0.304
  Chirality :  0.035   0.306   1567
  Planarity :  0.004   0.055    787
  Dihedral  : 24.125 177.185   3725
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  9.88 %
    Favored  : 89.24 %
  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:  1.11 (0.42), residues: 393
  helix:  2.17 (0.46), residues: 121
  sheet:  0.08 (0.64), residues: 74
  loop :  0.19 (0.43), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 363 
 TYR   0.011   0.001   TYR D 327 
 PHE   0.006   0.001   PHE D 453 
 TRP   0.007   0.001   TRP D 161 
 HIS   0.003   0.001   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 8635)
  covalent geometry    : angle       0.56126 (12736)
  hydrogen bonds       : bond        0.03912 (  314)
  hydrogen bonds       : angle       3.22664 (  694)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.184 
Fit side-chains
REVERT: D   37 ARG cc_start: 0.8424 (ttp80) cc_final: 0.7837 (ttp-110)
REVERT: D  355 LYS cc_start: 0.8693 (mmpt) cc_final: 0.8460 (mtmm)
REVERT: D  392 LYS cc_start: 0.8601 (mptt) cc_final: 0.8374 (mmtp)
  outliers start: 3
  outliers final: 1
  residues processed: 29
  average time/residue: 0.8334
  time to fit residues: 25.3201
Evaluate side-chains
  27 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  351 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0870
   chunk 13 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 41 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    1.1160

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

Flipped N/Q/H residues before XYZ refinement:
** D  87 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 = 0.3326 r_free = 0.3326 target = 0.085565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.060478 restraints weight = 16834.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 1.46
r_work: 0.2720 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2615 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.1514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8635  Z= 0.177
  Angle     :  0.555   6.800  12736  Z= 0.301
  Chirality :  0.035   0.302   1567
  Planarity :  0.004   0.054    787
  Dihedral  : 24.112 177.177   3725
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  9.59 %
    Favored  : 89.53 %
  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:  1.03 (0.42), residues: 393
  helix:  2.18 (0.46), residues: 121
  sheet:  0.44 (0.72), residues: 61
  loop : -0.08 (0.41), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 363 
 TYR   0.009   0.001   TYR D 484 
 PHE   0.007   0.001   PHE D 453 
 TRP   0.007   0.001   TRP D 161 
 HIS   0.003   0.001   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 8635)
  covalent geometry    : angle       0.55514 (12736)
  hydrogen bonds       : bond        0.03905 (  314)
  hydrogen bonds       : angle       3.21921 (  694)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.161 
Fit side-chains
REVERT: D   37 ARG cc_start: 0.8491 (ttp80) cc_final: 0.7906 (ttp-110)
REVERT: D  392 LYS cc_start: 0.8597 (mptt) cc_final: 0.8370 (mmtp)
  outliers start: 3
  outliers final: 2
  residues processed: 29
  average time/residue: 0.8009
  time to fit residues: 24.3459
Evaluate side-chains
  27 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   68 MET
Chi-restraints excluded: chain D residue  351 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** D  87 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 = 0.3299 r_free = 0.3299 target = 0.084116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.058889 restraints weight = 16844.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.2800 rms_B_bonded: 1.45
r_work: 0.2681 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2576 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.1416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   8635  Z= 0.246
  Angle     :  0.592   6.738  12736  Z= 0.320
  Chirality :  0.037   0.338   1567
  Planarity :  0.004   0.054    787
  Dihedral  : 24.132 177.139   3725
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  9.88 %
    Favored  : 89.24 %
  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:  0.98 (0.42), residues: 393
  helix:  2.14 (0.47), residues: 119
  sheet:  0.15 (0.66), residues: 70
  loop : -0.00 (0.41), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 363 
 TYR   0.013   0.001   TYR D 327 
 PHE   0.007   0.001   PHE D 453 
 TRP   0.008   0.001   TRP D 161 
 HIS   0.002   0.001   HIS D 428 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 8635)
  covalent geometry    : angle       0.59221 (12736)
  hydrogen bonds       : bond        0.04217 (  314)
  hydrogen bonds       : angle       3.31393 (  694)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 0.191 
Fit side-chains
REVERT: D   37 ARG cc_start: 0.8500 (ttp80) cc_final: 0.7902 (ttp-110)
REVERT: D  355 LYS cc_start: 0.8668 (mmpt) cc_final: 0.8463 (mtmm)
REVERT: D  392 LYS cc_start: 0.8597 (mptt) cc_final: 0.8375 (mmtp)
  outliers start: 3
  outliers final: 2
  residues processed: 27
  average time/residue: 0.7485
  time to fit residues: 21.2148
Evaluate side-chains
  28 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 26
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   68 MET
Chi-restraints excluded: chain D residue  351 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 56 optimal weight:   10.0000
   chunk 59 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 39 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** D  87 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 = 0.3302 r_free = 0.3302 target = 0.084268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.058976 restraints weight = 16827.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.2802 rms_B_bonded: 1.45
r_work: 0.2684 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2579 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8635  Z= 0.229
  Angle     :  0.589   6.816  12736  Z= 0.318
  Chirality :  0.037   0.336   1567
  Planarity :  0.004   0.054    787
  Dihedral  : 24.132 177.157   3725
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  9.88 %
    Favored  : 89.24 %
  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:  0.97 (0.42), residues: 393
  helix:  2.14 (0.47), residues: 119
  sheet:  0.15 (0.66), residues: 70
  loop : -0.01 (0.41), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 363 
 TYR   0.009   0.001   TYR D   5 
 PHE   0.007   0.001   PHE D 453 
 TRP   0.008   0.001   TRP D 161 
 HIS   0.003   0.001   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 ( 8635)
  covalent geometry    : angle       0.58853 (12736)
  hydrogen bonds       : bond        0.04178 (  314)
  hydrogen bonds       : angle       3.31742 (  694)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2589.39 seconds
wall clock time: 44 minutes 41.89 seconds (2681.89 seconds total)