Starting phenix.real_space_refine
on Fri Dec  8 02:50:16 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo2_26638/12_2023/7uo2_26638.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo2_26638/12_2023/7uo2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo2_26638/12_2023/7uo2_26638.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo2_26638/12_2023/7uo2_26638.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo2_26638/12_2023/7uo2_26638.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo2_26638/12_2023/7uo2_26638.pdb"
  }
  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

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 6735
  Number of models: 1
  Model: ""
    Number of chains: 2
    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: 5813
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 5813
          Unusual residues: {' MG': 3}
          Classifications: {'RNA': 271, 'undetermined': 3}
          Modifications used: {'5*END': 1, 'rna2p_pur': 29, 'rna2p_pyr': 26, 'rna3p_pur': 122, 'rna3p_pyr': 94}
          Link IDs: {'rna2p': 55, 'rna3p': 215, None: 3}
            Not linked:
              pdbres="  U B 376 "
              pdbres=" MG B 401 "
            Not linked:
              pdbres=" MG B 401 "
              pdbres=" MG B 402 "
            Not linked:
              pdbres=" MG B 402 "
              pdbres=" MG B 403 "
          Chain breaks: 1
  Time building chain proxies: 4.49, per 1000 atoms: 0.67
  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  - 3.50
        Amino acid           : False - 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: 4.29
  Conformation dependent library (CDL) restraints added in 271.6 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: 3.49
  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: 2.44

  Time building geometry restraints manager: 4.29 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:
       98.91 -   105.92: 1458
      105.92 -   112.92: 4320
      112.92 -   119.93: 2689
      119.93 -   126.93: 2266
      126.93 -   133.93: 667
  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: 3901
       35.14 -    70.28: 665
       70.28 -   105.41: 98
      105.41 -   140.55: 4
      140.55 -   175.69: 4
  Dihedral angle restraints: 4672
    sinusoidal: 4347
      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 4669 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 2.440
  nonbonded pdb=" O2'   G B 262 "
            pdb=" OP1   U B 263 "
     model   vdw
     2.221 2.440
  ... (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
========== 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:             2.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          10.660
  Check model and map are aligned:         0.120
  Set scattering table:                    0.060
  Process input model:                     25.570
  Find NCS groups from input model:        0.120
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.180
-------------------------------------------------------------------------------
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  : 25.921 175.688   4458
  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 fitting.
    rotamer outliers: 2
    poor density    : 28
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 30
  average time/residue: 0.2561
  time to fit residues: 9.6865
Evaluate side-chains
  18 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.318 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.2411
-------------------------------------------------------------------------------
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:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 29 optimal weight:    9.9990
   chunk 11 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 34 optimal weight:    3.9990
   chunk 10 optimal weight:    0.1980
   overall best weight:    2.5986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.3882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   7440  Z= 0.374
  Angle     :  0.881   7.172  11400  Z= 0.439
  Chirality :  0.045   0.262   1493
  Planarity :  0.007   0.038    435
  Dihedral  : 26.683 176.131   4213
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 27.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.55 %
    Favored  : 85.45 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 15.31 %
    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: -3.41 (0.69), residues: 110
  helix: -0.92 (0.80), residues: 39
  sheet: -1.59 (1.26), residues: 14
  loop : -3.58 (0.65), 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  43 
   PHE   0.014   0.003   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
  24 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 23
  average time/residue: 0.2998
  time to fit residues: 8.5067
Evaluate side-chains
  20 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 19
  time to evaluate  : 0.266 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0587
  time to fit residues: 0.3442
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 23 optimal weight:    9.9990
   chunk 9 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.5230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.072   7440  Z= 0.487
  Angle     :  1.001   7.795  11400  Z= 0.489
  Chirality :  0.051   0.261   1493
  Planarity :  0.007   0.038    435
  Dihedral  : 27.208 171.825   4213
  Min Nonbonded Distance : 1.844

Molprobity Statistics.
  All-atom Clashscore : 35.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.36 %
    Favored  : 83.64 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 17.35 %
    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: -3.49 (0.72), residues: 110
  helix: -1.57 (0.72), residues: 40
  sheet: -1.48 (1.20), residues: 14
  loop : -3.20 (0.78), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.002   TRP A 108 
   HIS   0.006   0.003   HIS A  43 
   PHE   0.011   0.003   PHE A  84 
   ARG   0.005   0.001   ARG A  73 

*********************** 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
  23 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
  outliers start: 4
  outliers final: 1
  residues processed: 22
  average time/residue: 0.2930
  time to fit residues: 8.0402
Evaluate side-chains
  18 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 17
  time to evaluate  : 0.263 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0561
  time to fit residues: 0.3151
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 23 optimal weight:    9.9990
   chunk 34 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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  31 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.5152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.057   7440  Z= 0.406
  Angle     :  0.900   7.842  11400  Z= 0.442
  Chirality :  0.046   0.254   1493
  Planarity :  0.007   0.041    435
  Dihedral  : 27.088 173.725   4213
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 31.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.45 %
    Favored  : 84.55 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 20.41 %
    Favored  : 74.49 %
  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: -3.17 (0.76), residues: 110
  helix: -1.23 (0.79), residues: 40
  sheet: -1.41 (1.17), residues: 14
  loop : -3.04 (0.83), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.004   0.002   TRP A 108 
   HIS   0.005   0.002   HIS A  43 
   PHE   0.011   0.003   PHE A  84 
   ARG   0.003   0.001   ARG A 113 

*********************** 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 fitting.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 3
  residues processed: 23
  average time/residue: 0.2760
  time to fit residues: 8.0589
Evaluate side-chains
  22 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 19
  time to evaluate  : 0.331 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0645
  time to fit residues: 0.6177
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.5197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   7440  Z= 0.378
  Angle     :  0.883   7.713  11400  Z= 0.436
  Chirality :  0.045   0.257   1493
  Planarity :  0.007   0.043    435
  Dihedral  : 27.079 173.469   4213
  Min Nonbonded Distance : 1.844

Molprobity Statistics.
  All-atom Clashscore : 29.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.27 %
    Favored  : 82.73 %
  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: -3.58 (0.72), residues: 110
  helix: -1.59 (0.75), residues: 46
  sheet: -1.75 (1.03), residues: 14
  loop : -3.36 (0.78), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.003   TRP A 108 
   HIS   0.004   0.002   HIS A  43 
   PHE   0.010   0.003   PHE A  17 
   ARG   0.003   0.001   ARG A 113 

*********************** 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
  25 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 20
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 1
  residues processed: 24
  average time/residue: 0.2600
  time to fit residues: 7.9366
Evaluate side-chains
  20 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 19
  time to evaluate  : 0.296 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0719
  time to fit residues: 0.3622
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 26 optimal weight:   10.0000
   overall best weight:    2.3788

-------------------------------------------------------------------------------
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  31 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.5180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   7440  Z= 0.354
  Angle     :  0.863   7.646  11400  Z= 0.427
  Chirality :  0.045   0.265   1493
  Planarity :  0.006   0.042    435
  Dihedral  : 27.055 173.712   4213
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 28.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.45 %
    Favored  : 84.55 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 20.41 %
    Favored  : 74.49 %
  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: -3.07 (0.77), residues: 110
  helix: -1.04 (0.83), residues: 40
  sheet: -1.65 (1.11), residues: 14
  loop : -2.97 (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  84 
   ARG   0.004   0.001   ARG A  56 

*********************** 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
  27 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 4
  residues processed: 24
  average time/residue: 0.2554
  time to fit residues: 7.7404
Evaluate side-chains
  23 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.269 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0600
  time to fit residues: 0.6638
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 22 optimal weight:    8.9990
   chunk 16 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9990
   chunk 23 optimal weight:    9.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.5572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.060   7440  Z= 0.410
  Angle     :  0.937   7.749  11400  Z= 0.461
  Chirality :  0.048   0.293   1493
  Planarity :  0.007   0.053    435
  Dihedral  : 27.155 173.838   4213
  Min Nonbonded Distance : 1.839

Molprobity Statistics.
  All-atom Clashscore : 32.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.27 %
    Favored  : 82.73 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 21.43 %
    Favored  : 75.51 %
  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: -3.05 (0.77), residues: 110
  helix: -1.15 (0.83), residues: 40
  sheet: -1.31 (1.04), residues: 14
  loop : -2.96 (0.84), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.003   TRP A 108 
   HIS   0.005   0.003   HIS A 111 
   PHE   0.010   0.002   PHE A  84 
   ARG   0.004   0.001   ARG A 113 

*********************** 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
  25 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 25
  average time/residue: 0.2220
  time to fit residues: 7.3058
Evaluate side-chains
  20 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 19
  time to evaluate  : 0.294 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0613
  time to fit residues: 0.3527
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 3 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 26 optimal weight:   10.0000
   chunk 10 optimal weight:    0.6980
   overall best weight:    2.7388

-------------------------------------------------------------------------------
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  31 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.5546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059   7440  Z= 0.399
  Angle     :  0.908   7.580  11400  Z= 0.446
  Chirality :  0.046   0.284   1493
  Planarity :  0.007   0.047    435
  Dihedral  : 27.115 174.787   4213
  Min Nonbonded Distance : 1.840

Molprobity Statistics.
  All-atom Clashscore : 30.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.45 %
    Favored  : 84.55 %
  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: -3.00 (0.79), residues: 110
  helix: -1.08 (0.85), residues: 40
  sheet: -1.34 (0.96), residues: 14
  loop : -2.93 (0.86), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.005   TRP A 108 
   HIS   0.005   0.002   HIS A 111 
   PHE   0.010   0.002   PHE A  19 
   ARG   0.003   0.001   ARG A 113 

*********************** 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
  26 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 22
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 2
  residues processed: 23
  average time/residue: 0.2706
  time to fit residues: 7.8788
Evaluate side-chains
  21 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.307 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0646
  time to fit residues: 0.5081
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 22 optimal weight:    8.9990
   chunk 36 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 23 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.5757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.060   7440  Z= 0.412
  Angle     :  0.943   7.650  11400  Z= 0.463
  Chirality :  0.048   0.285   1493
  Planarity :  0.007   0.054    435
  Dihedral  : 27.214 175.189   4213
  Min Nonbonded Distance : 1.833

Molprobity Statistics.
  All-atom Clashscore : 33.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.27 %
    Favored  : 82.73 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 25.51 %
    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: -2.88 (0.80), residues: 110
  helix: -0.89 (0.87), residues: 40
  sheet: -1.27 (1.01), residues: 14
  loop : -2.95 (0.86), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.004   TRP A 108 
   HIS   0.005   0.002   HIS A 111 
   PHE   0.011   0.003   PHE A  19 
   ARG   0.003   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
  21 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 20
  average time/residue: 0.2511
  time to fit residues: 6.5096
Evaluate side-chains
  20 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.301 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.2435
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 23 optimal weight:    9.9990
   chunk 32 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 4 optimal weight:    0.7980
   chunk 8 optimal weight:    0.3980
   chunk 30 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.5009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   7440  Z= 0.217
  Angle     :  0.736   6.530  11400  Z= 0.367
  Chirality :  0.037   0.267   1493
  Planarity :  0.005   0.038    435
  Dihedral  : 26.784 176.780   4213
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 22.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.73 %
    Favored  : 87.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 28.57 %
    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: -2.55 (0.79), residues: 110
  helix: -0.66 (0.87), residues: 40
  sheet: -1.14 (1.04), residues: 14
  loop : -2.69 (0.84), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.004   0.001   TRP A 108 
   HIS   0.004   0.002   HIS A  59 
   PHE   0.010   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
  21 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.2985
  time to fit residues: 7.7830
Evaluate side-chains
  20 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.304 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.2569
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 1 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 23 optimal weight:   10.0000
   chunk 14 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    3.3988

-------------------------------------------------------------------------------
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 = 0.3926 r_free = 0.3926 target = 0.059371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.046026 restraints weight = 55663.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 1.73
r_work: 0.3328 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.5884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.068   7440  Z= 0.488
  Angle     :  1.007   7.636  11400  Z= 0.490
  Chirality :  0.050   0.283   1493
  Planarity :  0.007   0.056    435
  Dihedral  : 27.235 175.251   4213
  Min Nonbonded Distance : 1.813

Molprobity Statistics.
  All-atom Clashscore : 35.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.09 %
    Favored  : 80.91 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 26.53 %
    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: -2.86 (0.80), residues: 110
  helix: -0.97 (0.86), residues: 40
  sheet: -1.29 (0.99), residues: 14
  loop : -2.84 (0.88), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.004   TRP A 108 
   HIS   0.006   0.003   HIS A 111 
   PHE   0.012   0.003   PHE A  19 
   ARG   0.004   0.001   ARG A 113 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1420.74 seconds
wall clock time: 26 minutes 56.28 seconds (1616.28 seconds total)