Starting phenix.real_space_refine
on Tue Feb 11 23:55:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uo2_26638/02_2025/7uo2_26638.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uo2_26638/02_2025/7uo2_26638.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uo2_26638/02_2025/7uo2_26638.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uo2_26638/02_2025/7uo2_26638.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uo2_26638/02_2025/7uo2_26638.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uo2_26638/02_2025/7uo2_26638.cif"
  }
  resolution = 3.1
  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=   0.012
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
     P     270      5.49       5
     Mg      3      5.21       5
     S       2      5.16       5
     C    3171      2.51       5
     N    1258      2.21       5
     O    2031      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6735
  Number of models: 1
  Model: ""
    Number of chains: 3
    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: 5810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 5810
          Classifications: {'RNA': 271}
          Modifications used: {'5*END': 1, 'rna2p_pur': 29, 'rna2p_pyr': 26, 'rna3p_pur': 122, 'rna3p_pyr': 94}
          Link IDs: {'rna2p': 55, 'rna3p': 215}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 5.49, per 1000 atoms: 0.82
  Number of scatterers: 6735
  At special positions: 0
  Unit cell: (88.5636, 124.96, 127.386, 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)
     S       2     16.00
     P     270     15.00
     Mg      3     11.99
     O    2031      8.00
     N    1258      7.00
     C    3171      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.58
  Conformation dependent library (CDL) restraints added in 330.9 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, 9.8% beta
      81 base pairs and 119 stacking pairs defined.
    Time for finding SS restraints: 3.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 10
      removed outlier: 3.850A  pdb=" N   LEU A   9 " --> pdb=" O   PRO A   6 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG A  10 " --> pdb=" O   ARG A   7 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 6 through 10'
    Processing helix  chain 'A' and resid 13 through 23
      removed outlier: 4.134A  pdb=" N   PHE A  17 " --> pdb=" O   THR A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 73
      removed outlier: 3.956A  pdb=" N   ASN A  62 " --> pdb=" O   ALA A  58 " (cutoff:3.500A)
      removed outlier: 5.619A  pdb=" N   ILE A  64 " --> pdb=" O   GLU A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 108
      removed outlier: 3.504A  pdb=" N   LEU A 100 " --> pdb=" O   ASP A  96 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU A 107 " --> pdb=" O   ALA A 103 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   TRP A 108 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35
      removed outlier: 3.850A  pdb=" N   THR A  33 " --> pdb=" O   VAL A  87 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   VAL A  87 " --> pdb=" O   THR A  33 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   ARG A  45 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 8.273A  pdb=" N   VAL A  86 " --> pdb=" O   ARG A  45 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 8.931A  pdb=" N   ALA A  88 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)

    24 hydrogen bonds defined for protein.
    72 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      218 hydrogen bonds
      400 hydrogen bond angles
      0 basepair planarities
      81 basepair parallelities
      119 stacking parallelities
  Total time for adding SS restraints: 2.27

  Time building geometry restraints manager: 1.88 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 570
        1.32 -     1.44: 3614
        1.44 -     1.56: 2714
        1.56 -     1.69: 539
        1.69 -     1.81: 3
  Bond restraints: 7440
  Sorted by residual:
  bond pdb=" C2'   U B  17 "
       pdb=" C1'   U B  17 "
    ideal  model  delta    sigma   weight residual
    1.529  1.508  0.021 1.50e-02 4.44e+03 1.88e+00
  bond pdb=" C4'   U B  17 "
       pdb=" C3'   U B  17 "
    ideal  model  delta    sigma   weight residual
    1.521  1.540 -0.019 1.50e-02 4.44e+03 1.62e+00
  bond pdb=" O3'   U B  17 "
       pdb=" P     C B  18 "
    ideal  model  delta    sigma   weight residual
    1.607  1.624 -0.017 1.50e-02 4.44e+03 1.31e+00
  bond pdb=" O4'   G B 271 "
       pdb=" C1'   G B 271 "
    ideal  model  delta    sigma   weight residual
    1.412  1.429 -0.017 1.50e-02 4.44e+03 1.23e+00
  bond pdb=" C4'   G B 271 "
       pdb=" C3'   G B 271 "
    ideal  model  delta    sigma   weight residual
    1.521  1.505  0.016 1.50e-02 4.44e+03 1.17e+00
  ... (remaining 7435 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 11105
        1.49 -     2.98: 235
        2.98 -     4.47: 49
        4.47 -     5.96: 10
        5.96 -     7.44: 1
  Bond angle restraints: 11400
  Sorted by residual:
  angle pdb=" C2'   G B 271 "
        pdb=" C1'   G B 271 "
        pdb=" N9    G B 271 "
      ideal   model   delta    sigma   weight residual
     112.00  106.53    5.47 1.50e+00 4.44e-01 1.33e+01
  angle pdb=" C4'   U B  17 "
        pdb=" C3'   U B  17 "
        pdb=" O3'   U B  17 "
      ideal   model   delta    sigma   weight residual
     113.00  117.92   -4.92 1.50e+00 4.44e-01 1.08e+01
  angle pdb=" O4'   G B 271 "
        pdb=" C4'   G B 271 "
        pdb=" C3'   G B 271 "
      ideal   model   delta    sigma   weight residual
     104.00  100.99    3.01 1.00e+00 1.00e+00 9.05e+00
  angle pdb=" C4'   G B 271 "
        pdb=" C3'   G B 271 "
        pdb=" O3'   G B 271 "
      ideal   model   delta    sigma   weight residual
     113.00  117.45   -4.45 1.50e+00 4.44e-01 8.78e+00
  angle pdb=" O4'   G B 271 "
        pdb=" C1'   G B 271 "
        pdb=" N9    G B 271 "
      ideal   model   delta    sigma   weight residual
     108.50  112.90   -4.40 1.50e+00 4.44e-01 8.59e+00
  ... (remaining 11395 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.14: 4005
       35.14 -    70.28: 745
       70.28 -   105.41: 98
      105.41 -   140.55: 4
      140.55 -   175.69: 4
  Dihedral angle restraints: 4856
    sinusoidal: 4531
      harmonic: 325
  Sorted by residual:
  dihedral pdb=" O4'   U B 257 "
           pdb=" C1'   U B 257 "
           pdb=" N1    U B 257 "
           pdb=" C2    U B 257 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   51.23  148.77     1      1.50e+01 4.44e-03 7.92e+01
  dihedral pdb=" O4'   U B 331 "
           pdb=" C1'   U B 331 "
           pdb=" N1    U B 331 "
           pdb=" C2    U B 331 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   47.69 -175.69     1      1.70e+01 3.46e-03 6.63e+01
  dihedral pdb=" O4'   U B 302 "
           pdb=" C1'   U B 302 "
           pdb=" N1    U B 302 "
           pdb=" C2    U B 302 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   58.14  173.86     1      1.70e+01 3.46e-03 6.62e+01
  ... (remaining 4853 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1424
       0.058 -    0.116: 58
       0.116 -    0.174: 9
       0.174 -    0.232: 1
       0.232 -    0.290: 1
  Chirality restraints: 1493
  Sorted by residual:
  chirality pdb=" C3'   G B 271 "
            pdb=" C4'   G B 271 "
            pdb=" O3'   G B 271 "
            pdb=" C2'   G B 271 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.19   -0.29 2.00e-01 2.50e+01 2.10e+00
  chirality pdb=" C1'   G B  16 "
            pdb=" O4'   G B  16 "
            pdb=" C2'   G B  16 "
            pdb=" N9    G B  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.66   -0.20 2.00e-01 2.50e+01 1.00e+00
  chirality pdb=" C1'   G B 324 "
            pdb=" O4'   G B 324 "
            pdb=" C2'   G B 324 "
            pdb=" N9    G B 324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.29    0.17 2.00e-01 2.50e+01 6.86e-01
  ... (remaining 1490 not shown)

  Planarity restraints: 435
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B 271 "    0.053 2.00e-02 2.50e+03   2.45e-02 1.81e+01
        pdb=" N9    G B 271 "   -0.064 2.00e-02 2.50e+03
        pdb=" C8    G B 271 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7    G B 271 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    G B 271 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G B 271 "   -0.002 2.00e-02 2.50e+03
        pdb=" O6    G B 271 "    0.017 2.00e-02 2.50e+03
        pdb=" N1    G B 271 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    G B 271 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G B 271 "    0.000 2.00e-02 2.50e+03
        pdb=" N3    G B 271 "   -0.008 2.00e-02 2.50e+03
        pdb=" C4    G B 271 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B  17 "    0.015 2.00e-02 2.50e+03   2.20e-02 1.09e+01
        pdb=" N1    U B  17 "    0.014 2.00e-02 2.50e+03
        pdb=" C2    U B  17 "   -0.028 2.00e-02 2.50e+03
        pdb=" O2    U B  17 "   -0.013 2.00e-02 2.50e+03
        pdb=" N3    U B  17 "    0.037 2.00e-02 2.50e+03
        pdb=" C4    U B  17 "   -0.029 2.00e-02 2.50e+03
        pdb=" O4    U B  17 "    0.021 2.00e-02 2.50e+03
        pdb=" C5    U B  17 "   -0.018 2.00e-02 2.50e+03
        pdb=" C6    U B  17 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  16 "   -0.042 2.00e-02 2.50e+03   1.73e-02 8.95e+00
        pdb=" N9    G B  16 "    0.030 2.00e-02 2.50e+03
        pdb=" C8    G B  16 "    0.011 2.00e-02 2.50e+03
        pdb=" N7    G B  16 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    G B  16 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G B  16 "   -0.011 2.00e-02 2.50e+03
        pdb=" O6    G B  16 "   -0.017 2.00e-02 2.50e+03
        pdb=" N1    G B  16 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    G B  16 "    0.014 2.00e-02 2.50e+03
        pdb=" N2    G B  16 "   -0.006 2.00e-02 2.50e+03
        pdb=" N3    G B  16 "    0.008 2.00e-02 2.50e+03
        pdb=" C4    G B  16 "    0.007 2.00e-02 2.50e+03
  ... (remaining 432 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.61: 175
        2.61 -     3.18: 5207
        3.18 -     3.75: 13421
        3.75 -     4.33: 16769
        4.33 -     4.90: 22869
  Nonbonded interactions: 58441
  Sorted by model distance:
  nonbonded pdb=" OP1   G B 250 "
            pdb="MG    MG B 403 "
     model   vdw
     2.033 2.170
  nonbonded pdb=" OP1   A B  67 "
            pdb="MG    MG B 401 "
     model   vdw
     2.049 2.170
  nonbonded pdb=" OP1   A B 351 "
            pdb="MG    MG B 401 "
     model   vdw
     2.066 2.170
  nonbonded pdb=" O2'   A B 112 "
            pdb=" OP1   C B 115 "
     model   vdw
     2.134 3.040
  nonbonded pdb=" O2'   G B 262 "
            pdb=" OP1   U B 263 "
     model   vdw
     2.221 3.040
  ... (remaining 58436 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.890
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7109
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   7440  Z= 0.115
  Angle     :  0.549   7.444  11400  Z= 0.273
  Chirality :  0.027   0.290   1493
  Planarity :  0.004   0.035    435
  Dihedral  : 26.442 175.688   4642
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  1.82 %
    Allowed  : 14.55 %
    Favored  : 83.64 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 10.20 %
    Favored  : 87.76 %
  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: -3.16 (0.70), residues: 110
  helix: -0.20 (0.84), residues: 36
  sheet: -1.26 (1.44), residues: 14
  loop : -3.74 (0.58), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP A 108 
 HIS   0.002   0.000   HIS A  59 
 PHE   0.004   0.001   PHE A   5 
 ARG   0.002   0.000   ARG A  69 

*********************** 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
  30 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 28
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 30
  average time/residue: 0.2514
  time to fit residues: 9.4452
Evaluate side-chains
  18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 15 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 29 optimal weight:   10.0000
   chunk 11 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 22 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   chunk 10 optimal weight:    0.4980
   overall best weight:    3.0988

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.061067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.047542 restraints weight = 54082.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 1.45
r_work: 0.3375 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.3976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.076   7440  Z= 0.457
  Angle     :  0.946   8.602  11400  Z= 0.468
  Chirality :  0.047   0.272   1493
  Planarity :  0.008   0.046    435
  Dihedral  : 27.310 175.344   4397
  Min Nonbonded Distance : 1.819

Molprobity Statistics.
  All-atom Clashscore : 21.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.36 %
    Favored  : 83.64 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 14.29 %
    Favored  : 81.63 %
  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: -3.34 (0.69), residues: 110
  helix: -0.89 (0.76), residues: 39
  sheet: -1.44 (1.27), residues: 14
  loop : -3.54 (0.66), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.002   TRP A 108 
 HIS   0.006   0.003   HIS A 111 
 PHE   0.024   0.004   PHE A  19 
 ARG   0.007   0.001   ARG A  10 

*********************** 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
  25 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.271 
Fit side-chains
REVERT: A   31 GLN cc_start: 0.8352 (tp-100) cc_final: 0.7995 (tp-100)
REVERT: A  105 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7641 (mm-30)
  outliers start: 4
  outliers final: 2
  residues processed: 24
  average time/residue: 0.2384
  time to fit residues: 7.4558
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  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 SER
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  105 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 23 optimal weight:    9.9990
   chunk 6 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  59 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.061234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.047689 restraints weight = 56215.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 1.30
r_work: 0.3387 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.4255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   7440  Z= 0.328
  Angle     :  0.818   7.089  11400  Z= 0.405
  Chirality :  0.042   0.257   1493
  Planarity :  0.007   0.049    435
  Dihedral  : 27.203 173.408   4397
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 18.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.73 %
    Favored  : 87.27 %
  Rotamer:
    Outliers :  8.16 %
    Allowed  : 14.29 %
    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 (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: -3.56 (0.72), residues: 110
  helix: -1.35 (0.76), residues: 45
  sheet: -1.73 (1.14), residues: 14
  loop : -3.57 (0.75), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 108 
 HIS   0.004   0.002   HIS A  43 
 PHE   0.010   0.002   PHE A  17 
 ARG   0.005   0.001   ARG A  56 

*********************** 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
  29 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 21
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A   10 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.7051 (mtt180)
REVERT: A   31 GLN cc_start: 0.8231 (tp-100) cc_final: 0.7841 (tp-100)
  outliers start: 8
  outliers final: 4
  residues processed: 26
  average time/residue: 0.3028
  time to fit residues: 9.6071
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  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ARG
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  112 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 27 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 26 optimal weight:    9.9990
   chunk 29 optimal weight:    5.9990
   chunk 10 optimal weight:    0.2980
   chunk 25 optimal weight:    3.9990
   overall best weight:    2.4186

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

Flipped N/Q/H residues before XYZ refinement:
** A  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.060594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.047046 restraints weight = 57122.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 1.36
r_work: 0.3364 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.4805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064   7440  Z= 0.365
  Angle     :  0.872   7.455  11400  Z= 0.432
  Chirality :  0.045   0.275   1493
  Planarity :  0.007   0.037    435
  Dihedral  : 27.330 173.171   4397
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 22.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.64 %
    Favored  : 86.36 %
  Rotamer:
    Outliers :  8.16 %
    Allowed  : 15.31 %
    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: -3.52 (0.73), residues: 110
  helix: -1.47 (0.75), residues: 45
  sheet: -1.37 (1.15), residues: 14
  loop : -3.49 (0.79), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 108 
 HIS   0.004   0.002   HIS A  43 
 PHE   0.008   0.002   PHE A  84 
 ARG   0.004   0.001   ARG A  56 

*********************** 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
  26 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 18
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A   10 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7165 (mtt180)
REVERT: A   31 GLN cc_start: 0.8350 (tp-100) cc_final: 0.7832 (tp-100)
  outliers start: 8
  outliers final: 1
  residues processed: 25
  average time/residue: 0.1955
  time to fit residues: 6.5114
Evaluate side-chains
  19 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 17
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ARG
Chi-restraints excluded: chain A residue  112 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.061703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.048155 restraints weight = 55698.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 1.22
r_work: 0.3406 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.4447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7440  Z= 0.250
  Angle     :  0.750   6.569  11400  Z= 0.375
  Chirality :  0.039   0.255   1493
  Planarity :  0.006   0.037    435
  Dihedral  : 27.089 173.978   4397
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 16.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.82 %
    Favored  : 88.18 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 22.45 %
    Favored  : 73.47 %
  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: -3.23 (0.75), residues: 110
  helix: -1.24 (0.77), residues: 46
  sheet: -1.19 (1.17), residues: 14
  loop : -3.37 (0.81), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 108 
 HIS   0.003   0.001   HIS A  43 
 PHE   0.007   0.002   PHE A  19 
 ARG   0.004   0.001   ARG A  10 

*********************** 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
  24 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 20
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A   31 GLN cc_start: 0.8216 (tp-100) cc_final: 0.7737 (tp-100)
  outliers start: 4
  outliers final: 2
  residues processed: 23
  average time/residue: 0.2248
  time to fit residues: 6.7384
Evaluate side-chains
  21 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  112 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 23 optimal weight:   10.0000
   chunk 7 optimal weight:    0.0970
   chunk 1 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    2.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 111 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.060789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.047307 restraints weight = 56219.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 1.27
r_work: 0.3373 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.4879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066   7440  Z= 0.338
  Angle     :  0.843   7.185  11400  Z= 0.419
  Chirality :  0.044   0.264   1493
  Planarity :  0.006   0.038    435
  Dihedral  : 27.268 173.019   4397
  Min Nonbonded Distance : 1.867

Molprobity Statistics.
  All-atom Clashscore : 20.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.64 %
    Favored  : 86.36 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 23.47 %
    Favored  : 72.45 %
  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: -2.86 (0.77), residues: 110
  helix: -1.00 (0.81), residues: 40
  sheet: -1.15 (1.14), residues: 14
  loop : -2.85 (0.83), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 108 
 HIS   0.004   0.002   HIS A  43 
 PHE   0.009   0.002   PHE A  19 
 ARG   0.003   0.001   ARG A  10 

*********************** 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
  23 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A   31 GLN cc_start: 0.8253 (tp-100) cc_final: 0.7743 (tp-100)
REVERT: A  108 TRP cc_start: 0.7746 (m-10) cc_final: 0.7284 (m-10)
  outliers start: 4
  outliers final: 2
  residues processed: 22
  average time/residue: 0.2329
  time to fit residues: 6.6502
Evaluate side-chains
  21 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  112 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 7 optimal weight:    0.0980
   chunk 5 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 27 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   overall best weight:    1.8188

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

Flipped N/Q/H residues before XYZ refinement:
** A  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.061311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.047884 restraints weight = 55639.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 1.24
r_work: 0.3391 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.4771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   7440  Z= 0.284
  Angle     :  0.782   6.755  11400  Z= 0.390
  Chirality :  0.041   0.258   1493
  Planarity :  0.006   0.037    435
  Dihedral  : 27.174 173.275   4397
  Min Nonbonded Distance : 1.880

Molprobity Statistics.
  All-atom Clashscore : 17.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.82 %
    Favored  : 88.18 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 22.45 %
    Favored  : 73.47 %
  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: -2.76 (0.77), residues: 110
  helix: -0.91 (0.83), residues: 40
  sheet: -1.19 (1.15), residues: 14
  loop : -2.77 (0.83), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 108 
 HIS   0.004   0.002   HIS A  43 
 PHE   0.009   0.002   PHE A  19 
 ARG   0.002   0.000   ARG A 109 

*********************** 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
  23 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A   31 GLN cc_start: 0.8229 (tp-100) cc_final: 0.7831 (tp40)
REVERT: A  108 TRP cc_start: 0.7653 (m-10) cc_final: 0.7207 (m-10)
  outliers start: 4
  outliers final: 2
  residues processed: 22
  average time/residue: 0.2025
  time to fit residues: 6.1417
Evaluate side-chains
  21 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  112 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 11 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.059582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.046187 restraints weight = 56591.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 1.74
r_work: 0.3342 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.5522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.089   7440  Z= 0.468
  Angle     :  0.994   8.230  11400  Z= 0.486
  Chirality :  0.050   0.275   1493
  Planarity :  0.007   0.038    435
  Dihedral  : 27.585 172.288   4397
  Min Nonbonded Distance : 1.823

Molprobity Statistics.
  All-atom Clashscore : 25.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.36 %
    Favored  : 83.64 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 24.49 %
    Favored  : 72.45 %
  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: -3.15 (0.77), residues: 110
  helix: -1.27 (0.82), residues: 40
  sheet: -1.52 (1.08), residues: 14
  loop : -2.93 (0.83), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP A 108 
 HIS   0.006   0.003   HIS A  43 
 PHE   0.012   0.003   PHE A  19 
 ARG   0.003   0.001   ARG A  56 

*********************** 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: 3
    poor density    : 20
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A   31 GLN cc_start: 0.8253 (tp-100) cc_final: 0.7840 (tp40)
REVERT: A  108 TRP cc_start: 0.7832 (m-10) cc_final: 0.7308 (m-10)
REVERT: A  109 ARG cc_start: 0.8452 (mtm110) cc_final: 0.7829 (mmp80)
  outliers start: 3
  outliers final: 2
  residues processed: 22
  average time/residue: 0.2286
  time to fit residues: 6.5958
Evaluate side-chains
  21 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  112 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 11 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.060752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.047249 restraints weight = 56423.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 1.23
r_work: 0.3376 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.5133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   7440  Z= 0.311
  Angle     :  0.829   7.208  11400  Z= 0.413
  Chirality :  0.043   0.263   1493
  Planarity :  0.006   0.037    435
  Dihedral  : 27.314 172.831   4397
  Min Nonbonded Distance : 1.867

Molprobity Statistics.
  All-atom Clashscore : 18.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.82 %
    Favored  : 88.18 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 25.51 %
    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: -2.88 (0.79), residues: 110
  helix: -1.04 (0.85), residues: 40
  sheet: -1.23 (1.13), residues: 14
  loop : -2.82 (0.85), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 108 
 HIS   0.004   0.002   HIS A  43 
 PHE   0.011   0.002   PHE A  19 
 ARG   0.002   0.000   ARG A  56 

*********************** 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
  23 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 20
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A   31 GLN cc_start: 0.8294 (tp-100) cc_final: 0.7839 (tp40)
REVERT: A  108 TRP cc_start: 0.7739 (m-10) cc_final: 0.7214 (m-10)
  outliers start: 3
  outliers final: 2
  residues processed: 23
  average time/residue: 0.1737
  time to fit residues: 5.5312
Evaluate side-chains
  21 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  112 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 29 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 23 optimal weight:    9.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3995 r_free = 0.3995 target = 0.061740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.048317 restraints weight = 56650.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 1.18
r_work: 0.3416 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.4739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7440  Z= 0.226
  Angle     :  0.736   8.381  11400  Z= 0.370
  Chirality :  0.038   0.263   1493
  Planarity :  0.005   0.036    435
  Dihedral  : 27.068 174.514   4397
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 15.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.82 %
    Favored  : 88.18 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 27.55 %
    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: -2.56 (0.80), residues: 110
  helix: -0.78 (0.86), residues: 40
  sheet: -0.92 (1.26), residues: 14
  loop : -2.67 (0.84), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP A 108 
 HIS   0.003   0.001   HIS A  43 
 PHE   0.009   0.002   PHE A  19 
 ARG   0.002   0.000   ARG A  69 

********************** 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
  24 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.8258 (tp-100) cc_final: 0.7874 (tp-100)
  outliers start: 2
  outliers final: 1
  residues processed: 24
  average time/residue: 0.2665
  time to fit residues: 8.0435
Evaluate side-chains
  21 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 29 optimal weight:    9.9990
   chunk 36 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 24 optimal weight:    5.9990
   chunk 23 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    2.1186

-------------------------------------------------------------------------------
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 = 0.3968 r_free = 0.3968 target = 0.060808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.047409 restraints weight = 56308.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 1.28
r_work: 0.3378 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.5125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   7440  Z= 0.326
  Angle     :  0.834   7.552  11400  Z= 0.414
  Chirality :  0.043   0.266   1493
  Planarity :  0.006   0.037    435
  Dihedral  : 27.221 173.073   4397
  Min Nonbonded Distance : 1.877

Molprobity Statistics.
  All-atom Clashscore : 18.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.73 %
    Favored  : 87.27 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 28.57 %
    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: -2.68 (0.80), residues: 110
  helix: -0.90 (0.87), residues: 40
  sheet: -0.91 (1.20), residues: 14
  loop : -2.76 (0.84), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 108 
 HIS   0.004   0.002   HIS A 111 
 PHE   0.011   0.002   PHE A  19 
 ARG   0.003   0.000   ARG A 109 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5130.58 seconds
wall clock time: 91 minutes 21.73 seconds (5481.73 seconds total)