Starting phenix.real_space_refine
on Fri Feb 14 22:04:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uo0_26636/02_2025/7uo0_26636.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uo0_26636/02_2025/7uo0_26636.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uo0_26636/02_2025/7uo0_26636.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uo0_26636/02_2025/7uo0_26636.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uo0_26636/02_2025/7uo0_26636.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uo0_26636/02_2025/7uo0_26636.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      7      9.91       5
     P     454      5.49       5
     S       2      5.16       5
     C    4935      2.51       5
     N    1996      2.21       5
     O    3303      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10697
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 922
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 922
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 6, 'TRANS': 105}
    Chain: "B"
      Number of atoms: 8024
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 373, 8024
          Classifications: {'RNA': 373}
          Modifications used: {'5*END': 1, 'rna2p_pur': 27, 'rna2p_pyr': 26, 'rna3p_pur': 191, 'rna3p_pyr': 128}
          Link IDs: {'rna2p': 53, 'rna3p': 319}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 1744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 1744
          Classifications: {'RNA': 82}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 8, 'rna3p_pur': 37, 'rna3p_pyr': 33}
          Link IDs: {'rna2p': 11, 'rna3p': 70}
    Chain: "B"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Unusual residues: {' CA': 7}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
  Residues with excluded nonbonded symmetry interactions: 47
    residue:
      pdb=" P     C B  20 " occ=0.00
      ... (18 atoms not shown)
      pdb=" C6    C B  20 " occ=0.00
    residue:
      pdb=" P     C B  21 " occ=0.00
      ... (18 atoms not shown)
      pdb=" C6    C B  21 " occ=0.00
    residue:
      pdb=" P     G B  22 " occ=0.00
      ... (21 atoms not shown)
      pdb=" C4    G B  22 " occ=0.00
    residue:
      pdb=" P     C B  23 " occ=0.00
      ... (18 atoms not shown)
      pdb=" C6    C B  23 " occ=0.00
    residue:
      pdb=" P     U B  24 " occ=0.00
      ... (18 atoms not shown)
      pdb=" C6    U B  24 " occ=0.00
    residue:
      pdb=" P     U B  25 " occ=0.00
      ... (18 atoms not shown)
      pdb=" C6    U B  25 " occ=0.00
    residue:
      pdb=" P     C B  26 " occ=0.00
      ... (18 atoms not shown)
      pdb=" C6    C B  26 " occ=0.00
    residue:
      pdb=" P     G B  27 " occ=0.00
      ... (21 atoms not shown)
      pdb=" C4    G B  27 " occ=0.00
    residue:
      pdb=" P     U B  28 " occ=0.00
      ... (18 atoms not shown)
      pdb=" C6    U B  28 " occ=0.00
    residue:
      pdb=" P     C B  29 " occ=0.00
      ... (18 atoms not shown)
      pdb=" C6    C B  29 " occ=0.00
    residue:
      pdb=" P     G B  30 " occ=0.00
      ... (21 atoms not shown)
      pdb=" C4    G B  30 " occ=0.00
    residue:
      pdb=" P     U B  31 " occ=0.00
      ... (18 atoms not shown)
      pdb=" C6    U B  31 " occ=0.00
    ... (remaining 35 not shown)
  Time building chain proxies: 7.27, per 1000 atoms: 0.68
  Number of scatterers: 10697
  At special positions: 0
  Unit cell: (125.902, 115.322, 194.672, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      7     19.99
     S       2     16.00
     P     454     15.00
     O    3303      8.00
     N    1996      7.00
     C    4935      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: 2.45
  Conformation dependent library (CDL) restraints added in 201.0 milliseconds
  

  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
      40.2% alpha, 11.6% beta
      113 base pairs and 83 stacking pairs defined.
    Time for finding SS restraints: 4.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 10
    Processing helix  chain 'A' and resid 13 through 23
      removed outlier: 3.778A  pdb=" N   PHE A  17 " --> pdb=" O   THR A  13 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   GLN A  23 " --> pdb=" O   PHE A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 75
    Processing helix  chain 'A' and resid 96 through 109
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28
      removed outlier: 3.739A  pdb=" N   GLY A  36 " --> pdb=" O   GLN A  25 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA A  27 " --> pdb=" O   ILE A  34 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 8.903A  pdb=" N   ALA A  88 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)

    34 hydrogen bonds defined for protein.
    93 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      312 hydrogen bonds
      598 hydrogen bond angles
      0 basepair planarities
      113 basepair parallelities
      83 stacking parallelities
  Total time for adding SS restraints: 3.77

  Time building geometry restraints manager: 2.96 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1461
        1.33 -     1.45: 5697
        1.45 -     1.57: 3806
        1.57 -     1.69: 907
        1.69 -     1.81: 3
  Bond restraints: 11874
  Sorted by residual:
  bond pdb=" C3'   G C  19 "
       pdb=" O3'   G C  19 "
    ideal  model  delta    sigma   weight residual
    1.417  1.440 -0.023 1.50e-02 4.44e+03 2.27e+00
  bond pdb=" C1'   C B  35 "
       pdb=" N1    C B  35 "
    ideal  model  delta    sigma   weight residual
    1.470  1.492 -0.022 1.50e-02 4.44e+03 2.14e+00
  bond pdb=" C3'   G B 137 "
       pdb=" O3'   G B 137 "
    ideal  model  delta    sigma   weight residual
    1.417  1.438 -0.021 1.50e-02 4.44e+03 2.04e+00
  bond pdb=" C1'   G B 190 "
       pdb=" N9    G B 190 "
    ideal  model  delta    sigma   weight residual
    1.465  1.486 -0.021 1.50e-02 4.44e+03 2.03e+00
  bond pdb=" C3'   A B 352 "
       pdb=" O3'   A B 352 "
    ideal  model  delta    sigma   weight residual
    1.417  1.438 -0.021 1.50e-02 4.44e+03 1.96e+00
  ... (remaining 11869 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    15.47: 18310
       15.47 -    30.94: 4
       30.94 -    46.41: 0
       46.41 -    61.88: 0
       61.88 -    77.35: 5
  Bond angle restraints: 18319
  Sorted by residual:
  angle pdb=" O3'   C B  14 "
        pdb=" P     A B  15 "
        pdb=" OP1   A B  15 "
      ideal   model   delta    sigma   weight residual
     108.00   30.65   77.35 3.00e+00 1.11e-01 6.65e+02
  angle pdb=" O3'   A B  15 "
        pdb=" P     G B  16 "
        pdb=" OP1   G B  16 "
      ideal   model   delta    sigma   weight residual
     108.00   34.51   73.49 3.00e+00 1.11e-01 6.00e+02
  angle pdb=" O3'   A B 130 "
        pdb=" P     C B 131 "
        pdb=" OP1   C B 131 "
      ideal   model   delta    sigma   weight residual
     108.00   34.71   73.29 3.00e+00 1.11e-01 5.97e+02
  angle pdb=" O3'   C B  70 "
        pdb=" P     C B  71 "
        pdb=" OP1   C B  71 "
      ideal   model   delta    sigma   weight residual
     108.00   35.06   72.94 3.00e+00 1.11e-01 5.91e+02
  angle pdb=" O3'   C B 252 "
        pdb=" P     C B 253 "
        pdb=" OP1   C B 253 "
      ideal   model   delta    sigma   weight residual
     108.00   36.18   71.82 3.00e+00 1.11e-01 5.73e+02
  ... (remaining 18314 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.89: 6290
       35.89 -    71.77: 1215
       71.77 -   107.66: 181
      107.66 -   143.55: 28
      143.55 -   179.43: 31
  Dihedral angle restraints: 7745
    sinusoidal: 7420
      harmonic: 325
  Sorted by residual:
  dihedral pdb=" C4'   C C  63 "
           pdb=" C3'   C C  63 "
           pdb=" C2'   C C  63 "
           pdb=" C1'   C C  63 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   36.41  -71.41     1      8.00e+00 1.56e-02 1.02e+02
  dihedral pdb=" C4'   G B 190 "
           pdb=" C3'   G B 190 "
           pdb=" C2'   G B 190 "
           pdb=" C1'   G B 190 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   36.38  -71.38     1      8.00e+00 1.56e-02 1.02e+02
  dihedral pdb=" C4'   C C  49 "
           pdb=" C3'   C C  49 "
           pdb=" C2'   C C  49 "
           pdb=" C1'   C C  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   35.89  -70.89     1      8.00e+00 1.56e-02 1.01e+02
  ... (remaining 7742 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.180: 2098
       0.180 -    0.360: 286
       0.360 -    0.540: 22
       0.540 -    0.721: 2
       0.721 -    0.901: 4
  Chirality restraints: 2412
  Sorted by residual:
  chirality pdb=" P     C B 253 "
            pdb=" OP1   C B 253 "
            pdb=" OP2   C B 253 "
            pdb=" O5'   C B 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    1.51    0.90 2.00e-01 2.50e+01 2.03e+01
  chirality pdb=" P     C B  71 "
            pdb=" OP1   C B  71 "
            pdb=" OP2   C B  71 "
            pdb=" O5'   C B  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    1.52    0.89 2.00e-01 2.50e+01 1.98e+01
  chirality pdb=" P     C B 131 "
            pdb=" OP1   C B 131 "
            pdb=" OP2   C B 131 "
            pdb=" O5'   C B 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    1.58    0.83 2.00e-01 2.50e+01 1.71e+01
  ... (remaining 2409 not shown)

  Planarity restraints: 619
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B  35 "   -0.001 2.00e-02 2.50e+03   1.40e-02 4.43e+00
        pdb=" N1    C B  35 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    C B  35 "    0.034 2.00e-02 2.50e+03
        pdb=" O2    C B  35 "   -0.022 2.00e-02 2.50e+03
        pdb=" N3    C B  35 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    C B  35 "    0.004 2.00e-02 2.50e+03
        pdb=" N4    C B  35 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5    C B  35 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    C B  35 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  63 "   -0.004 2.00e-02 2.50e+03   1.09e-02 3.54e+00
        pdb=" N9    G B  63 "    0.002 2.00e-02 2.50e+03
        pdb=" C8    G B  63 "    0.004 2.00e-02 2.50e+03
        pdb=" N7    G B  63 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    G B  63 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    G B  63 "   -0.001 2.00e-02 2.50e+03
        pdb=" O6    G B  63 "   -0.001 2.00e-02 2.50e+03
        pdb=" N1    G B  63 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    G B  63 "   -0.028 2.00e-02 2.50e+03
        pdb=" N2    G B  63 "    0.024 2.00e-02 2.50e+03
        pdb=" N3    G B  63 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    G B  63 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C  53 "    0.022 2.00e-02 2.50e+03   1.04e-02 3.25e+00
        pdb=" N9    G C  53 "   -0.028 2.00e-02 2.50e+03
        pdb=" C8    G C  53 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    G C  53 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    G C  53 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    G C  53 "    0.001 2.00e-02 2.50e+03
        pdb=" O6    G C  53 "    0.005 2.00e-02 2.50e+03
        pdb=" N1    G C  53 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    G C  53 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G C  53 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    G C  53 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    G C  53 "    0.000 2.00e-02 2.50e+03
  ... (remaining 616 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 640
        2.67 -     3.23: 8176
        3.23 -     3.79: 17008
        3.79 -     4.34: 18215
        4.34 -     4.90: 27169
  Nonbonded interactions: 71208
  Sorted by model distance:
  nonbonded pdb=" O4    U B  97 "
            pdb=" N6    A B  99 "
     model   vdw
     2.117 3.120
  nonbonded pdb=" O4    U B  25 "
            pdb=" O6    G B  56 "
     model   vdw
     2.129 2.432
  nonbonded pdb=" O2'   G B 291 "
            pdb=" OP2   G B 293 "
     model   vdw
     2.139 3.040
  nonbonded pdb=" O2'   A B 248 "
            pdb=" O2'   A C  74 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" O2'   U B 366 "
            pdb=" O5'   C B 367 "
     model   vdw
     2.207 3.040
  ... (remaining 71203 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:             6.120
  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:          0.440
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     27.970
  Find NCS groups from input model:        0.080
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3191
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      :  0.003   0.024  11874  Z= 0.176
  Angle     :  2.227  77.348  18319  Z= 0.847
  Chirality :  0.111   0.901   2412
  Planarity :  0.004   0.029    619
  Dihedral  : 29.933 179.431   7531
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  7.14 %
    Favored  : 90.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.84), residues: 110
  helix:  1.29 (0.81), residues: 45
  sheet: -0.19 (1.14), residues: 12
  loop : -1.41 (0.95), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP A 108 
 HIS   0.004   0.002   HIS A  77 
 PHE   0.011   0.002   PHE A  72 
 ARG   0.005   0.000   ARG A  75 

*********************** 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
****************************
Evaluate side-chains
  23 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 21
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.6386 (mmt) cc_final: 0.5867 (tpp)
  outliers start: 2
  outliers final: 0
  residues processed: 22
  average time/residue: 0.2858
  time to fit residues: 8.6153
Evaluate side-chains
  11 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 14 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 43 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 26 optimal weight:    9.9990
   chunk 32 optimal weight:    4.9990
   chunk 50 optimal weight:    8.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
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 = 0.4872 r_free = 0.4872 target = 0.145760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.126127 restraints weight = 88875.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.4374 rms_B_bonded: 4.15
r_work (final): 0.4374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5362
moved from start:          1.0597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.065  11874  Z= 0.558
  Angle     :  1.590  12.386  18319  Z= 0.752
  Chirality :  0.069   0.423   2412
  Planarity :  0.013   0.209    619
  Dihedral  : 31.096 176.180   7286
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 30.77
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  :  5.45 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  8.16 %
    Allowed  : 13.27 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.76), residues: 110
  helix: -1.10 (0.73), residues: 40
  sheet: -0.95 (0.99), residues: 29
  loop : -1.49 (0.93), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.004   TRP A 108 
 HIS   0.032   0.010   HIS A 111 
 PHE   0.024   0.006   PHE A  21 
 ARG   0.014   0.002   ARG A  73 

*********************** 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
****************************
Evaluate side-chains
  27 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 19
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 3
  residues processed: 26
  average time/residue: 0.3883
  time to fit residues: 12.7717
Evaluate side-chains
  14 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 11
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  107 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 0 optimal weight:    0.6980
   chunk 47 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.4586

-------------------------------------------------------------------------------
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 = 0.4901 r_free = 0.4901 target = 0.148106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4580 r_free = 0.4580 target = 0.128795 restraints weight = 89134.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.4428 rms_B_bonded: 1.64
r_work (final): 0.4428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5273
moved from start:          1.0995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  11874  Z= 0.221
  Angle     :  0.886   9.510  18319  Z= 0.421
  Chirality :  0.041   0.224   2412
  Planarity :  0.007   0.099    619
  Dihedral  : 30.331 178.278   7286
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.81), residues: 110
  helix: -1.03 (0.74), residues: 46
  sheet: -1.31 (0.98), residues: 29
  loop : -1.37 (1.14), residues: 35

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP A 108 
 HIS   0.009   0.003   HIS A  59 
 PHE   0.022   0.005   PHE A  19 
 ARG   0.016   0.001   ARG A  98 

*********************** 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
****************************
Evaluate side-chains
  22 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 17
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 2
  residues processed: 21
  average time/residue: 0.3298
  time to fit residues: 9.1338
Evaluate side-chains
  16 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  107 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 11 optimal weight:    8.9990
   chunk 14 optimal weight:   10.0000
   chunk 44 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 37 optimal weight:    7.9990
   chunk 5 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    2.3386

-------------------------------------------------------------------------------
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 = 0.4598 r_free = 0.4598 target = 0.128434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.117436 restraints weight = 93738.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.4336 rms_B_bonded: 1.69
r_work (final): 0.4336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5438
moved from start:          1.3997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  11874  Z= 0.330
  Angle     :  1.022  10.060  18319  Z= 0.489
  Chirality :  0.046   0.263   2412
  Planarity :  0.007   0.049    619
  Dihedral  : 30.547 177.966   7286
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 17.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 24.49 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.85 (0.69), residues: 110
  helix: -1.39 (0.67), residues: 39
  sheet: -2.03 (0.87), residues: 30
  loop : -2.00 (0.87), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.001   TRP A 108 
 HIS   0.006   0.002   HIS A  59 
 PHE   0.016   0.004   PHE A  19 
 ARG   0.014   0.002   ARG A  98 

*********************** 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
****************************
Evaluate side-chains
  21 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 17
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 2
  residues processed: 20
  average time/residue: 0.3793
  time to fit residues: 9.8952
Evaluate side-chains
  18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 16
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue  107 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 50 optimal weight:    9.9990
   chunk 39 optimal weight:    7.9990
   chunk 19 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 22 optimal weight:    8.9990
   chunk 11 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    3.5388

-------------------------------------------------------------------------------
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 = 0.4477 r_free = 0.4477 target = 0.120902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.109018 restraints weight = 93381.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.4185 rms_B_bonded: 2.19
r_work (final): 0.4185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5827
moved from start:          1.8120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.079  11874  Z= 0.452
  Angle     :  1.227  11.660  18319  Z= 0.589
  Chirality :  0.056   0.302   2412
  Planarity :  0.008   0.048    619
  Dihedral  : 31.228 178.500   7286
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 27.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.13 (0.74), residues: 110
  helix: -1.54 (0.67), residues: 44
  sheet: -2.04 (0.89), residues: 31
  loop : -2.42 (1.05), residues: 35

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.004   TRP A 108 
 HIS   0.005   0.001   HIS A  59 
 PHE   0.072   0.006   PHE A  19 
 ARG   0.011   0.001   ARG A  57 

*********************** 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
****************************
Evaluate side-chains
  21 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 16
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 4
  residues processed: 18
  average time/residue: 0.2170
  time to fit residues: 5.9500
Evaluate side-chains
  18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 14
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  108 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 23 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9980
   chunk 28 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   overall best weight:    2.3786

-------------------------------------------------------------------------------
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 = 0.4489 r_free = 0.4489 target = 0.121452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.109414 restraints weight = 90655.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.4207 rms_B_bonded: 1.50
r_work (final): 0.4207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5790
moved from start:          1.8862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  11874  Z= 0.296
  Angle     :  0.920  10.366  18319  Z= 0.448
  Chirality :  0.044   0.295   2412
  Planarity :  0.006   0.057    619
  Dihedral  : 30.807 176.350   7286
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 16.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 26.53 %
    Favored  : 69.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.48 (0.75), residues: 110
  helix: -0.88 (0.72), residues: 46
  sheet: -2.11 (0.83), residues: 31
  loop : -1.85 (1.05), residues: 33

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 108 
 HIS   0.009   0.003   HIS A  59 
 PHE   0.020   0.004   PHE A  21 
 ARG   0.004   0.001   ARG A  37 

*********************** 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
****************************
Evaluate side-chains
  22 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 18
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
  outliers start: 4
  outliers final: 2
  residues processed: 21
  average time/residue: 0.2587
  time to fit residues: 7.6958
Evaluate side-chains
  18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 16
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  107 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 8 optimal weight:    0.8980
   chunk 27 optimal weight:   10.0000
   chunk 40 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 45 optimal weight:    4.9990
   chunk 50 optimal weight:   10.0000
   chunk 19 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    3.1788

-------------------------------------------------------------------------------
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 = 0.4406 r_free = 0.4406 target = 0.116275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.103877 restraints weight = 93147.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.4101 rms_B_bonded: 2.11
r_work (final): 0.4101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6059
moved from start:          2.0711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.098  11874  Z= 0.423
  Angle     :  1.134  12.589  18319  Z= 0.545
  Chirality :  0.052   0.355   2412
  Planarity :  0.007   0.047    619
  Dihedral  : 31.326 177.668   7286
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 25.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 27.55 %
    Favored  : 66.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.02 (0.74), residues: 110
  helix: -1.34 (0.71), residues: 40
  sheet: -2.58 (0.75), residues: 31
  loop : -1.86 (1.07), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.004   TRP A 108 
 HIS   0.006   0.002   HIS A  77 
 PHE   0.076   0.007   PHE A  19 
 ARG   0.015   0.002   ARG A  73 

*********************** 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
****************************
Evaluate side-chains
  21 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 15
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8508 (mp0)
  outliers start: 6
  outliers final: 4
  residues processed: 19
  average time/residue: 0.2075
  time to fit residues: 6.2440
Evaluate side-chains
  18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 14
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  107 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 49 optimal weight:    9.9990
   chunk 2 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 26 optimal weight:    9.9990
   chunk 36 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 14 optimal weight:    9.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 111 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.115608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.103200 restraints weight = 92330.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.4094 rms_B_bonded: 1.59
r_work (final): 0.4094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6076
moved from start:          2.1972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063  11874  Z= 0.351
  Angle     :  1.013  10.751  18319  Z= 0.483
  Chirality :  0.047   0.329   2412
  Planarity :  0.006   0.049    619
  Dihedral  : 31.204 177.912   7286
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 21.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.91 %
    Favored  : 89.09 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 24.49 %
    Favored  : 69.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.77 (0.75), residues: 110
  helix: -1.04 (0.74), residues: 40
  sheet: -2.65 (0.74), residues: 31
  loop : -1.64 (1.07), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.003   TRP A 108 
 HIS   0.009   0.002   HIS A  59 
 PHE   0.053   0.005   PHE A  19 
 ARG   0.016   0.001   ARG A  73 

*********************** 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
****************************
Evaluate side-chains
  23 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 17
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 3
  residues processed: 21
  average time/residue: 0.2879
  time to fit residues: 8.2248
Evaluate side-chains
  20 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  107 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 53 optimal weight:   10.0000
   chunk 49 optimal weight:    9.9990
   chunk 9 optimal weight:    0.6980
   chunk 47 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    1.8586

-------------------------------------------------------------------------------
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 = 0.4417 r_free = 0.4417 target = 0.116256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.103796 restraints weight = 92932.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.4116 rms_B_bonded: 1.72
r_work (final): 0.4116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6018
moved from start:          2.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  11874  Z= 0.250
  Angle     :  0.874  11.038  18319  Z= 0.417
  Chirality :  0.041   0.283   2412
  Planarity :  0.007   0.104    619
  Dihedral  : 30.900 177.074   7286
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 16.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 25.51 %
    Favored  : 68.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.53 (0.77), residues: 110
  helix: -0.62 (0.75), residues: 39
  sheet: -2.88 (0.67), residues: 31
  loop : -1.42 (1.15), residues: 40

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 108 
 HIS   0.003   0.001   HIS A  77 
 PHE   0.066   0.005   PHE A  19 
 ARG   0.010   0.001   ARG A  73 

*********************** 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
****************************
Evaluate side-chains
  24 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 18
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8549 (tp30) cc_final: 0.8313 (tp30)
  outliers start: 6
  outliers final: 2
  residues processed: 22
  average time/residue: 0.3270
  time to fit residues: 9.6619
Evaluate side-chains
  16 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  107 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 29 optimal weight:    7.9990
   chunk 17 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 55 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   overall best weight:    3.5988

-------------------------------------------------------------------------------
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 = 0.4351 r_free = 0.4351 target = 0.112756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.100188 restraints weight = 94065.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.4027 rms_B_bonded: 2.16
r_work (final): 0.4027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6178
moved from start:          2.3410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061  11874  Z= 0.429
  Angle     :  1.146  12.818  18319  Z= 0.543
  Chirality :  0.053   0.347   2412
  Planarity :  0.010   0.181    619
  Dihedral  : 31.373 179.287   7286
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 27.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 28.57 %
    Favored  : 67.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.24 (0.77), residues: 110
  helix: -1.21 (0.69), residues: 39
  sheet: -3.46 (0.61), residues: 31
  loop : -1.61 (1.22), residues: 40

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.005   TRP A 108 
 HIS   0.003   0.002   HIS A  59 
 PHE   0.074   0.006   PHE A  19 
 ARG   0.014   0.002   ARG A  73 

********************** 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
****************************
Evaluate side-chains
  18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 14
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
  outliers start: 4
  outliers final: 2
  residues processed: 16
  average time/residue: 0.3087
  time to fit residues: 6.8940
Evaluate side-chains
  16 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  107 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 37 optimal weight:    9.9990
   chunk 15 optimal weight:   10.0000
   chunk 16 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 54 optimal weight:   10.0000
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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 = 0.4393 r_free = 0.4393 target = 0.114979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.102646 restraints weight = 93853.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.4085 rms_B_bonded: 1.69
r_work (final): 0.4085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6066
moved from start:          2.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  11874  Z= 0.253
  Angle     :  0.877  10.539  18319  Z= 0.418
  Chirality :  0.041   0.243   2412
  Planarity :  0.006   0.053    619
  Dihedral  : 30.873 177.794   7286
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 16.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 26.53 %
    Favored  : 70.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.91 (0.71), residues: 110
  helix: -0.85 (0.69), residues: 39
  sheet: -3.48 (0.58), residues: 31
  loop : -1.35 (1.06), residues: 40

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.004   TRP A 108 
 HIS   0.003   0.001   HIS A  77 
 PHE   0.065   0.004   PHE A  19 
 ARG   0.006   0.001   ARG A  73 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5661.03 seconds
wall clock time: 100 minutes 58.15 seconds (6058.15 seconds total)