Starting phenix.real_space_refine
on Sun Aug 24 02:16:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uo1_26637/08_2025/7uo1_26637.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uo1_26637/08_2025/7uo1_26637.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uo1_26637/08_2025/7uo1_26637.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uo1_26637/08_2025/7uo1_26637.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uo1_26637/08_2025/7uo1_26637.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uo1_26637/08_2025/7uo1_26637.map"
  }
  resolution = 3.2
  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
-------------------------------------------------------------------------------
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=  -0.000 sd=   1.000
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: 7
    Type Number    sf(0)   Gaussians
     Ca     10      9.91       5
     P     454      5.49       5
     S       2      5.16       5
     C    4934      2.51       5
     N    1993      2.21       5
     O    3301      1.98       5
     H    5894      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16588
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 12071
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 373, 12071
          Classifications: {'RNA': 373}
          Modifications used: {'3*END': 1, '5*END': 1, 'rna2p_pur': 25, 'rna2p_pyr': 26, 'rna3p_pur': 191, 'rna3p_pyr': 128}
          Link IDs: {'rna2p': 51, 'rna3p': 321}
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      Number of atoms: 2622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 2622
          Classifications: {'RNA': 82}
          Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 37, 'rna3p_pyr': 36}
          Link IDs: {'rna2p': 8, 'rna3p': 73}
    Chain: "A"
      Number of atoms: 1885
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 1885
          Classifications: {'peptide': 112}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 105}
    Chain: "B"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Unusual residues: {' CA': 10}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
  Residues with excluded nonbonded symmetry interactions: 46
    residue:
      pdb=" P     C B  20 " occ=0.00
      ... (29 atoms not shown)
      pdb=" H6    C B  20 " occ=0.00
    residue:
      pdb=" P     C B  21 " occ=0.00
      ... (29 atoms not shown)
      pdb=" H6    C B  21 " occ=0.00
    residue:
      pdb=" P     G B  22 " occ=0.00
      ... (32 atoms not shown)
      pdb=" H22   G B  22 " occ=0.00
    residue:
      pdb=" P     C B  23 " occ=0.00
      ... (29 atoms not shown)
      pdb=" H6    C B  23 " occ=0.00
    residue:
      pdb=" P     U B  24 " occ=0.00
      ... (28 atoms not shown)
      pdb=" H6    U B  24 " occ=0.00
    residue:
      pdb=" P     U B  25 " occ=0.00
      ... (28 atoms not shown)
      pdb=" H6    U B  25 " occ=0.00
    residue:
      pdb=" P     C B  26 " occ=0.00
      ... (29 atoms not shown)
      pdb=" H6    C B  26 " occ=0.00
    residue:
      pdb=" P     G B  27 " occ=0.00
      ... (32 atoms not shown)
      pdb=" H22   G B  27 " occ=0.00
    residue:
      pdb=" P     U B  28 " occ=0.00
      ... (28 atoms not shown)
      pdb=" H6    U B  28 " occ=0.00
    residue:
      pdb=" P     C B  29 " occ=0.00
      ... (29 atoms not shown)
      pdb=" H6    C B  29 " occ=0.00
    residue:
      pdb=" P     G B  30 " occ=0.00
      ... (32 atoms not shown)
      pdb=" H22   G B  30 " occ=0.00
    residue:
      pdb=" P     U B  31 " occ=0.00
      ... (28 atoms not shown)
      pdb=" H6    U B  31 " occ=0.00
    ... (remaining 34 not shown)
  Time building chain proxies: 2.74, per 1000 atoms: 0.17
  Number of scatterers: 16588
  At special positions: 0
  Unit cell: (99.6826, 116.048, 196.39, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Ca     10     19.99
     S       2     16.00
     P     454     15.00
     O    3301      8.00
     N    1993      7.00
     C    4934      6.00
     H    5894      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.35
  Conformation dependent library (CDL) restraints added in 197.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  214

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 1 sheets defined
      45.5% alpha, 13.4% beta
      109 base pairs and 164 stacking pairs defined.
    Time for finding SS restraints: 2.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 9
    Processing helix  chain 'A' and resid 12 through 21
      removed outlier: 3.528A  pdb=" N   PHE A  16 " --> pdb=" O   THR A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 74
    Processing helix  chain 'A' and resid 95 through 111
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27

    45 hydrogen bonds defined for protein.
    126 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      294 hydrogen bonds
      544 hydrogen bond angles
      0 basepair planarities
      109 basepair parallelities
      164 stacking parallelities
  Total time for adding SS restraints: 3.31

  Time building geometry restraints manager: 1.87 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 5893
        1.03 -     1.22: 78
        1.22 -     1.42: 5415
        1.42 -     1.61: 6364
        1.61 -     1.81: 11
  Bond restraints: 17761
  Sorted by residual:
  bond pdb=" C1'   C B  35 "
       pdb=" N1    C B  35 "
    ideal  model  delta    sigma   weight residual
    1.470  1.493 -0.023 1.50e-02 4.44e+03 2.39e+00
  bond pdb=" C1'   C B 131 "
       pdb=" N1    C B 131 "
    ideal  model  delta    sigma   weight residual
    1.470  1.491 -0.021 1.50e-02 4.44e+03 1.90e+00
  bond pdb=" C1'   C B 343 "
       pdb=" N1    C B 343 "
    ideal  model  delta    sigma   weight residual
    1.470  1.489 -0.019 1.50e-02 4.44e+03 1.60e+00
  bond pdb=" C1'   A C  14 "
       pdb=" N9    A C  14 "
    ideal  model  delta    sigma   weight residual
    1.465  1.484 -0.019 1.50e-02 4.44e+03 1.58e+00
  bond pdb=" C3'   G B  64 "
       pdb=" O3'   G B  64 "
    ideal  model  delta    sigma   weight residual
    1.417  1.435 -0.018 1.50e-02 4.44e+03 1.41e+00
  ... (remaining 17756 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    17.92: 31738
       17.92 -    35.84: 5
       35.84 -    53.77: 0
       53.77 -    71.69: 0
       71.69 -    89.61: 42
  Bond angle restraints: 31785
  Sorted by residual:
  angle pdb=" O3'   U B 299 "
        pdb=" P     G B 300 "
        pdb=" OP1   G B 300 "
      ideal   model   delta    sigma   weight residual
     108.00   18.39   89.61 3.00e+00 1.11e-01 8.92e+02
  angle pdb=" O3'   C B   9 "
        pdb=" P     C B  10 "
        pdb=" OP1   C B  10 "
      ideal   model   delta    sigma   weight residual
     108.00   18.82   89.18 3.00e+00 1.11e-01 8.84e+02
  angle pdb=" O3'   A B  13 "
        pdb=" P     C B  14 "
        pdb=" OP1   C B  14 "
      ideal   model   delta    sigma   weight residual
     108.00   18.84   89.16 3.00e+00 1.11e-01 8.83e+02
  angle pdb=" O3'   C C  75 "
        pdb=" P     C C  76 "
        pdb=" OP1   C C  76 "
      ideal   model   delta    sigma   weight residual
     108.00   19.12   88.88 3.00e+00 1.11e-01 8.78e+02
  angle pdb=" O3'   G B  19 "
        pdb=" P     C B  20 "
        pdb=" OP1   C B  20 "
      ideal   model   delta    sigma   weight residual
     108.00   19.22   88.78 3.00e+00 1.11e-01 8.76e+02
  ... (remaining 31780 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    36.00: 7509
       36.00 -    72.00: 1257
       72.00 -   108.00: 177
      108.00 -   143.99: 53
      143.99 -   179.99: 52
  Dihedral angle restraints: 9048
    sinusoidal: 8675
      harmonic: 373
  Sorted by residual:
  dihedral pdb=" C4'   G B 101 "
           pdb=" C3'   G B 101 "
           pdb=" C2'   G B 101 "
           pdb=" C1'   G B 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   36.25  -71.25     1      8.00e+00 1.56e-02 1.02e+02
  dihedral pdb=" C4'   A B 351 "
           pdb=" C3'   A B 351 "
           pdb=" C2'   A B 351 "
           pdb=" C1'   A B 351 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   36.20  -71.20     1      8.00e+00 1.56e-02 1.02e+02
  dihedral pdb=" C4'   G B 332 "
           pdb=" C3'   G B 332 "
           pdb=" C2'   G B 332 "
           pdb=" C1'   G B 332 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   35.79  -70.79     1      8.00e+00 1.56e-02 1.01e+02
  ... (remaining 9045 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.115: 2096
       0.115 -    0.231: 83
       0.231 -    0.346: 200
       0.346 -    0.461: 23
       0.461 -    0.577: 8
  Chirality restraints: 2410
  Sorted by residual:
  chirality pdb=" P     A B 233 "
            pdb=" OP1   A B 233 "
            pdb=" OP2   A B 233 "
            pdb=" O5'   A B 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    2.99   -0.58 2.00e-01 2.50e+01 8.31e+00
  chirality pdb=" P     C B  20 "
            pdb=" OP1   C B  20 "
            pdb=" OP2   C B  20 "
            pdb=" O5'   C B  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.95   -0.54 2.00e-01 2.50e+01 7.17e+00
  chirality pdb=" P     C B  14 "
            pdb=" OP1   C B  14 "
            pdb=" OP2   C B  14 "
            pdb=" O5'   C B  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.93   -0.52 2.00e-01 2.50e+01 6.88e+00
  ... (remaining 2407 not shown)

  Planarity restraints: 1097
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B  35 "   -0.030 2.00e-02 2.50e+03   1.54e-02 6.50e+00
        pdb=" N1    C B  35 "    0.031 2.00e-02 2.50e+03
        pdb=" C2    C B  35 "   -0.018 2.00e-02 2.50e+03
        pdb=" O2    C B  35 "    0.019 2.00e-02 2.50e+03
        pdb=" N3    C B  35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    C B  35 "   -0.004 2.00e-02 2.50e+03
        pdb=" N4    C B  35 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5    C B  35 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    C B  35 "    0.003 2.00e-02 2.50e+03
        pdb=" H5    C B  35 "   -0.000 2.00e-02 2.50e+03
        pdb=" H6    C B  35 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B 106 "   -0.008 2.00e-02 2.50e+03   1.18e-02 4.87e+00
        pdb=" N9    G B 106 "    0.004 2.00e-02 2.50e+03
        pdb=" C8    G B 106 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    G B 106 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G B 106 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G B 106 "    0.009 2.00e-02 2.50e+03
        pdb=" O6    G B 106 "   -0.012 2.00e-02 2.50e+03
        pdb=" N1    G B 106 "   -0.006 2.00e-02 2.50e+03
        pdb=" C2    G B 106 "    0.033 2.00e-02 2.50e+03
        pdb=" N2    G B 106 "   -0.022 2.00e-02 2.50e+03
        pdb=" N3    G B 106 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    G B 106 "   -0.002 2.00e-02 2.50e+03
        pdb=" H8    G B 106 "   -0.003 2.00e-02 2.50e+03
        pdb=" H1    G B 106 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C C  76 "   -0.018 2.00e-02 2.50e+03   1.26e-02 4.37e+00
        pdb=" N1    C C  76 "    0.018 2.00e-02 2.50e+03
        pdb=" C2    C C  76 "   -0.025 2.00e-02 2.50e+03
        pdb=" O2    C C  76 "    0.019 2.00e-02 2.50e+03
        pdb=" N3    C C  76 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    C C  76 "   -0.007 2.00e-02 2.50e+03
        pdb=" N4    C C  76 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    C C  76 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    C C  76 "    0.003 2.00e-02 2.50e+03
        pdb=" H5    C C  76 "    0.002 2.00e-02 2.50e+03
        pdb=" H6    C C  76 "    0.005 2.00e-02 2.50e+03
  ... (remaining 1094 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.21: 1249
        2.21 -     2.81: 22703
        2.81 -     3.41: 39051
        3.41 -     4.00: 52292
        4.00 -     4.60: 76175
  Nonbonded interactions: 191470
  Sorted by model distance:
  nonbonded pdb=" O6    G B  52 "
            pdb=" H   ARG A   6 "
     model   vdw
     1.615 2.450
  nonbonded pdb="HO2'   C B 138 "
            pdb=" O5'   A B 139 "
     model   vdw
     1.618 2.450
  nonbonded pdb="HO2'   G B  84 "
            pdb=" O5'   C B  85 "
     model   vdw
     1.632 2.450
  nonbonded pdb=" H62   A B  81 "
            pdb=" O2'   G B 280 "
     model   vdw
     1.635 2.450
  nonbonded pdb="HO2'   C B  35 "
            pdb=" OP2   C B  36 "
     model   vdw
     1.638 2.450
  ... (remaining 191465 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.91
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:             0.040
  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:             0.040
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     16.740
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5258
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      :  0.002   0.023  11867  Z= 0.154
  Angle     :  4.427  89.611  18304  Z= 1.518
  Chirality :  0.099   0.577   2410
  Planarity :  0.003   0.023    619
  Dihedral  : 31.568 179.992   7521
  Min Nonbonded Distance : 1.799

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  2.73 %
    Allowed  :  4.55 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.82), residues: 110
  helix:  2.24 (0.74), residues: 46
  sheet: -1.81 (0.82), residues: 30
  loop : -1.24 (1.17), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  56 
 PHE   0.003   0.000   PHE A  20 
 TRP   0.001   0.000   TRP A 107 
 HIS   0.002   0.000   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (11867)
  covalent geometry    : angle       4.42697 (18304)
  hydrogen bonds       : bond        0.07842 (  339)
  hydrogen bonds       : angle       3.08651 (  670)

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS    1 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Evaluate side-chains
  41 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 LEU cc_start: 0.7949 (mm) cc_final: 0.7600 (mm)
REVERT: A   72 ARG cc_start: 0.6821 (tpt90) cc_final: 0.6204 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.2362
  time to fit residues: 12.1189
Evaluate side-chains
  34 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 24 optimal weight:    7.9990
   chunk 48 optimal weight:    0.0970
   chunk 26 optimal weight:   20.0000
   chunk 2 optimal weight:    8.9990
   chunk 16 optimal weight:   20.0000
   chunk 32 optimal weight:    8.9990
   chunk 31 optimal weight:    8.9990
   chunk 25 optimal weight:   10.0000
   chunk 50 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    2.8184

-------------------------------------------------------------------------------
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 = 0.4944 r_free = 0.4944 target = 0.275403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4734 r_free = 0.4734 target = 0.249704 restraints weight = 48360.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.4616 rms_B_bonded: 1.00
r_work: 0.4385 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.4385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5895
moved from start:          0.3207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  11867  Z= 0.218
  Angle     :  1.901  30.621  18304  Z= 0.725
  Chirality :  0.255   2.274   2410
  Planarity :  0.005   0.048    619
  Dihedral  : 31.021 179.148   7276
  Min Nonbonded Distance : 1.867

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 12.24 %
    Favored  : 84.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.85), residues: 110
  helix:  2.22 (0.73), residues: 46
  sheet: -1.24 (0.83), residues: 30
  loop : -0.11 (1.36), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  97 
 PHE   0.011   0.002   PHE A  16 
 TRP   0.004   0.002   TRP A 107 
 HIS   0.003   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (11867)
  covalent geometry    : angle       1.90055 (18304)
  hydrogen bonds       : bond        0.08342 (  339)
  hydrogen bonds       : angle       2.69291 (  670)

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS    1 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Evaluate side-chains
  40 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLN cc_start: 0.7986 (mt0) cc_final: 0.7778 (mt0)
REVERT: A   72 ARG cc_start: 0.6419 (tpt90) cc_final: 0.5489 (tpt90)
  outliers start: 3
  outliers final: 3
  residues processed: 38
  average time/residue: 0.2746
  time to fit residues: 13.3149
Evaluate side-chains
  37 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   95 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 43 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   chunk 35 optimal weight:    6.9990
   chunk 24 optimal weight:    6.9990
   chunk 32 optimal weight:    7.9990
   chunk 30 optimal weight:    4.9990
   chunk 20 optimal weight:    9.9990
   chunk 48 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4754 r_free = 0.4754 target = 0.253179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.214690 restraints weight = 40853.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.4323 rms_B_bonded: 1.25
r_work: 0.4154 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.4154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6374
moved from start:          0.5870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  11867  Z= 0.317
  Angle     :  1.985  32.633  18304  Z= 0.749
  Chirality :  0.241   2.093   2410
  Planarity :  0.007   0.071    619
  Dihedral  : 31.275 179.630   7276
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 19.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 16.33 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.10 (0.84), residues: 110
  helix:  1.55 (0.72), residues: 46
  sheet: -1.31 (0.92), residues: 21
  loop : -1.15 (1.16), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  97 
 PHE   0.017   0.004   PHE A   4 
 TRP   0.004   0.002   TRP A 107 
 HIS   0.006   0.002   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00580 (11867)
  covalent geometry    : angle       1.98517 (18304)
  hydrogen bonds       : bond        0.09131 (  339)
  hydrogen bonds       : angle       3.43405 (  670)

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS    1 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Evaluate side-chains
  37 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.6727 (tpt90) cc_final: 0.4387 (tpt90)
  outliers start: 5
  outliers final: 4
  residues processed: 33
  average time/residue: 0.2319
  time to fit residues: 9.6099
Evaluate side-chains
  33 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   95 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 46 optimal weight:    0.5980
   chunk 41 optimal weight:   50.0000
   chunk 37 optimal weight:    6.9990
   chunk 10 optimal weight:    7.9990
   chunk 50 optimal weight:    6.9990
   chunk 8 optimal weight:   10.0000
   chunk 52 optimal weight:    7.9990
   chunk 19 optimal weight:    9.9990
   chunk 55 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    4.5188

-------------------------------------------------------------------------------
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 = 0.4718 r_free = 0.4718 target = 0.246509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.207073 restraints weight = 40480.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.4295 rms_B_bonded: 0.98
r_work: 0.4121 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.4121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6387
moved from start:          0.6831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11867  Z= 0.239
  Angle     :  1.901  30.654  18304  Z= 0.708
  Chirality :  0.246   2.156   2410
  Planarity :  0.006   0.035    619
  Dihedral  : 31.211 179.687   7276
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 14.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 20.41 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.87), residues: 110
  helix:  2.32 (0.77), residues: 46
  sheet: -1.27 (0.90), residues: 21
  loop : -1.52 (1.13), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A   9 
 PHE   0.009   0.002   PHE A   4 
 TRP   0.008   0.003   TRP A 107 
 HIS   0.006   0.003   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 (11867)
  covalent geometry    : angle       1.90055 (18304)
  hydrogen bonds       : bond        0.08203 (  339)
  hydrogen bonds       : angle       3.19482 (  670)

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS    1 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Evaluate side-chains
  30 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.6384 (tpt90) cc_final: 0.4089 (tpt90)
REVERT: A   97 ARG cc_start: 0.7143 (ttp80) cc_final: 0.6927 (tmm160)
  outliers start: 3
  outliers final: 2
  residues processed: 27
  average time/residue: 0.2917
  time to fit residues: 9.5924
Evaluate side-chains
  28 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 26
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   48 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 9 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 21 optimal weight:    8.9990
   chunk 47 optimal weight:    4.9990
   chunk 55 optimal weight:    6.9990
   chunk 36 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 46 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   overall best weight:    4.3188

-------------------------------------------------------------------------------
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 = 0.4688 r_free = 0.4688 target = 0.242879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.201620 restraints weight = 39733.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.4265 rms_B_bonded: 0.96
r_work: 0.4146 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.4146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6453
moved from start:          0.7457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030  11867  Z= 0.251
  Angle     :  1.913  29.288  18304  Z= 0.715
  Chirality :  0.244   2.092   2410
  Planarity :  0.006   0.049    619
  Dihedral  : 31.277 179.692   7276
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 16.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 16.33 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.86), residues: 110
  helix:  2.16 (0.77), residues: 46
  sheet: -1.16 (0.93), residues: 21
  loop : -1.39 (1.13), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 108 
 PHE   0.012   0.002   PHE A  18 
 TRP   0.005   0.002   TRP A 107 
 HIS   0.006   0.002   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 (11867)
  covalent geometry    : angle       1.91349 (18304)
  hydrogen bonds       : bond        0.08375 (  339)
  hydrogen bonds       : angle       3.37533 (  670)

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS    1 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Evaluate side-chains
  33 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 28
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.6432 (tpt90) cc_final: 0.4169 (tpt90)
  outliers start: 5
  outliers final: 4
  residues processed: 29
  average time/residue: 0.3224
  time to fit residues: 11.5321
Evaluate side-chains
  32 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   95 ASP
Chi-restraints excluded: chain A residue  110 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 20 optimal weight:    8.9990
   chunk 41 optimal weight:   50.0000
   chunk 42 optimal weight:   10.0000
   chunk 7 optimal weight:    6.9990
   chunk 30 optimal weight:    6.9990
   chunk 44 optimal weight:    8.9990
   chunk 53 optimal weight:    0.8980
   chunk 16 optimal weight:   20.0000
   chunk 55 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    4.5788

-------------------------------------------------------------------------------
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 = 0.4675 r_free = 0.4675 target = 0.241815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.202451 restraints weight = 39640.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.4266 rms_B_bonded: 1.03
r_work: 0.4091 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.4091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6439
moved from start:          0.7917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031  11867  Z= 0.254
  Angle     :  1.907  29.980  18304  Z= 0.711
  Chirality :  0.245   2.102   2410
  Planarity :  0.006   0.034    619
  Dihedral  : 31.251 178.046   7276
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 17.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 18.37 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.85), residues: 110
  helix:  2.22 (0.76), residues: 46
  sheet: -1.08 (0.95), residues: 21
  loop : -1.75 (1.08), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 108 
 PHE   0.009   0.002   PHE A  18 
 TRP   0.009   0.003   TRP A 107 
 HIS   0.006   0.002   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 (11867)
  covalent geometry    : angle       1.90748 (18304)
  hydrogen bonds       : bond        0.08275 (  339)
  hydrogen bonds       : angle       3.34789 (  670)

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS    1 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Evaluate side-chains
  33 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 28
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.6346 (tpt90) cc_final: 0.4103 (tpt90)
  outliers start: 5
  outliers final: 3
  residues processed: 29
  average time/residue: 0.3123
  time to fit residues: 11.3879
Evaluate side-chains
  30 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   95 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 21 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   chunk 51 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 25 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 39 optimal weight:   20.0000
   chunk 33 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 15 optimal weight:   20.0000
   chunk 19 optimal weight:    9.9990
   overall best weight:    6.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.238189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.198122 restraints weight = 39829.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.4203 rms_B_bonded: 1.32
r_work: 0.4041 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.4041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6524
moved from start:          0.8784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045  11867  Z= 0.364
  Angle     :  1.983  30.417  18304  Z= 0.755
  Chirality :  0.244   2.090   2410
  Planarity :  0.008   0.073    619
  Dihedral  : 31.538 179.445   7276
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 25.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 19.39 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.11 (0.77), residues: 110
  helix:  0.73 (0.69), residues: 46
  sheet: -1.36 (0.96), residues: 21
  loop : -2.00 (1.01), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 108 
 PHE   0.009   0.003   PHE A  71 
 TRP   0.008   0.004   TRP A 107 
 HIS   0.006   0.002   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00670 (11867)
  covalent geometry    : angle       1.98284 (18304)
  hydrogen bonds       : bond        0.10093 (  339)
  hydrogen bonds       : angle       3.96046 (  670)

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS    1 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Evaluate side-chains
  30 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.6416 (tpt90) cc_final: 0.4082 (tpt90)
  outliers start: 4
  outliers final: 4
  residues processed: 26
  average time/residue: 0.2528
  time to fit residues: 8.4680
Evaluate side-chains
  30 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   95 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 20 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   chunk 46 optimal weight:    2.9990
   chunk 39 optimal weight:   20.0000
   chunk 34 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   chunk 29 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 8 optimal weight:    9.9990
   chunk 21 optimal weight:    8.9990
   overall best weight:    6.9990

-------------------------------------------------------------------------------
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 = 0.4648 r_free = 0.4648 target = 0.237841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.197824 restraints weight = 39699.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.4209 rms_B_bonded: 1.26
r_work: 0.4040 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6524
moved from start:          0.9054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039  11867  Z= 0.349
  Angle     :  1.954  30.652  18304  Z= 0.737
  Chirality :  0.245   2.084   2410
  Planarity :  0.007   0.046    619
  Dihedral  : 31.471 179.123   7276
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 22.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 19.39 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.32 (0.79), residues: 110
  helix:  0.71 (0.71), residues: 46
  sheet: -1.71 (0.95), residues: 21
  loop : -2.17 (1.02), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  36 
 PHE   0.008   0.003   PHE A  18 
 TRP   0.008   0.004   TRP A 107 
 HIS   0.007   0.002   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00645 (11867)
  covalent geometry    : angle       1.95385 (18304)
  hydrogen bonds       : bond        0.09502 (  339)
  hydrogen bonds       : angle       3.78790 (  670)

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS    1 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Evaluate side-chains
  33 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.6448 (tpt90) cc_final: 0.4094 (tpt90)
REVERT: A   74 ARG cc_start: 0.7705 (tpp80) cc_final: 0.7356 (tpp80)
  outliers start: 4
  outliers final: 3
  residues processed: 29
  average time/residue: 0.2331
  time to fit residues: 8.7574
Evaluate side-chains
  31 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   48 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 8 optimal weight:    9.9990
   chunk 19 optimal weight:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 44 optimal weight:    8.9990
   chunk 36 optimal weight:    8.9990
   chunk 7 optimal weight:    4.9990
   chunk 25 optimal weight:    9.9990
   chunk 17 optimal weight:   10.0000
   chunk 40 optimal weight:   40.0000
   chunk 16 optimal weight:   20.0000
   overall best weight:    7.3990

-------------------------------------------------------------------------------
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 = 0.4630 r_free = 0.4630 target = 0.235397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.195030 restraints weight = 39315.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.4185 rms_B_bonded: 1.28
r_work: 0.4024 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.4024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6550
moved from start:          0.9431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045  11867  Z= 0.386
  Angle     :  1.989  30.767  18304  Z= 0.759
  Chirality :  0.244   2.067   2410
  Planarity :  0.008   0.075    619
  Dihedral  : 31.662 179.062   7276
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 25.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 19.39 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.89 (0.74), residues: 110
  helix:  0.01 (0.66), residues: 46
  sheet: -1.89 (0.95), residues: 21
  loop : -2.24 (0.97), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  36 
 PHE   0.011   0.003   PHE A  71 
 TRP   0.008   0.004   TRP A 107 
 HIS   0.007   0.003   HIS A 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00711 (11867)
  covalent geometry    : angle       1.98945 (18304)
  hydrogen bonds       : bond        0.10315 (  339)
  hydrogen bonds       : angle       4.02996 (  670)

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS    1 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Evaluate side-chains
  31 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 ARG cc_start: 0.7904 (mtt180) cc_final: 0.7638 (mtt180)
REVERT: A   72 ARG cc_start: 0.6557 (tpt90) cc_final: 0.4056 (tpt90)
REVERT: A   97 ARG cc_start: 0.7861 (ttp80) cc_final: 0.7635 (ttp80)
  outliers start: 3
  outliers final: 3
  residues processed: 28
  average time/residue: 0.2776
  time to fit residues: 9.6307
Evaluate side-chains
  31 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   48 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 13 optimal weight:   10.0000
   chunk 42 optimal weight:   10.0000
   chunk 4 optimal weight:   50.0000
   chunk 6 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   chunk 23 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 3 optimal weight:   30.0000
   chunk 0 optimal weight:   20.0000
   chunk 46 optimal weight:    0.9980
   chunk 11 optimal weight:    9.9990
   overall best weight:    3.5786

-------------------------------------------------------------------------------
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 = 0.4674 r_free = 0.4674 target = 0.240575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.200969 restraints weight = 39562.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.4242 rms_B_bonded: 0.89
r_work: 0.4083 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.4083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6453
moved from start:          0.9190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  11867  Z= 0.219
  Angle     :  1.899  28.743  18304  Z= 0.708
  Chirality :  0.246   2.127   2410
  Planarity :  0.006   0.037    619
  Dihedral  : 31.410 179.036   7276
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 15.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 20.41 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.85 (0.81), residues: 110
  helix:  1.47 (0.73), residues: 46
  sheet: -1.82 (0.92), residues: 21
  loop : -2.19 (1.01), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 108 
 PHE   0.009   0.002   PHE A   4 
 TRP   0.007   0.002   TRP A 107 
 HIS   0.005   0.002   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (11867)
  covalent geometry    : angle       1.89924 (18304)
  hydrogen bonds       : bond        0.08255 (  339)
  hydrogen bonds       : angle       3.45743 (  670)

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS    1 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Evaluate side-chains
  30 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.6328 (tpt90) cc_final: 0.4093 (tpt90)
  outliers start: 3
  outliers final: 3
  residues processed: 27
  average time/residue: 0.2575
  time to fit residues: 8.8345
Evaluate side-chains
  30 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   48 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 16 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 5 optimal weight:    9.9990
   chunk 41 optimal weight:   50.0000
   chunk 21 optimal weight:    8.9990
   chunk 54 optimal weight:    1.9990
   chunk 40 optimal weight:   40.0000
   chunk 35 optimal weight:    6.9990
   chunk 7 optimal weight:    4.9990
   chunk 1 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    5.9990

-------------------------------------------------------------------------------
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 = 0.4652 r_free = 0.4652 target = 0.237602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.197413 restraints weight = 39589.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.4201 rms_B_bonded: 1.20
r_work: 0.4037 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6520
moved from start:          0.9418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037  11867  Z= 0.319
  Angle     :  1.947  30.319  18304  Z= 0.734
  Chirality :  0.244   2.063   2410
  Planarity :  0.007   0.057    619
  Dihedral  : 31.538 178.295   7276
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 20.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 19.39 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.32 (0.77), residues: 110
  helix:  0.81 (0.69), residues: 46
  sheet: -1.94 (0.90), residues: 21
  loop : -2.16 (0.98), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 108 
 PHE   0.010   0.003   PHE A  71 
 TRP   0.008   0.003   TRP A 107 
 HIS   0.007   0.002   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00588 (11867)
  covalent geometry    : angle       1.94678 (18304)
  hydrogen bonds       : bond        0.09329 (  339)
  hydrogen bonds       : angle       3.77280 (  670)

===============================================================================
Job complete
usr+sys time: 4184.30 seconds
wall clock time: 71 minutes 48.35 seconds (4308.35 seconds total)