Starting phenix.real_space_refine
on Mon Mar 11 02:45:42 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo2_26638/03_2024/7uo2_26638.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo2_26638/03_2024/7uo2_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_26638/03_2024/7uo2_26638.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo2_26638/03_2024/7uo2_26638.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo2_26638/03_2024/7uo2_26638.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo2_26638/03_2024/7uo2_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-dev-5265/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: 4.18, per 1000 atoms: 0.62
  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: 3.67
  Conformation dependent library (CDL) restraints added in 220.7 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: 3.03
  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: 2.19

  Time building geometry restraints manager: 3.89 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: 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 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:             4.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          10.920
  Check model and map are aligned:         0.090
  Set scattering table:                    0.050
  Process input model:                     23.580
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  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:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.890
-------------------------------------------------------------------------------
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 fitting.
    rotamer outliers: 2
    poor density    : 28
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 30
  average time/residue: 0.2691
  time to fit residues: 10.1117
Evaluate side-chains
  18 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 29 optimal weight:   10.0000
   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:    2.7986

-------------------------------------------------------------------------------
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: 0.7672
moved from start:          0.3969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061   7440  Z= 0.416
  Angle     :  0.909   7.265  11400  Z= 0.451
  Chirality :  0.046   0.259   1493
  Planarity :  0.007   0.037    435
  Dihedral  : 27.194 176.725   4397
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 27.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.45 %
    Favored  : 84.55 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 15.31 %
    Favored  : 80.61 %
  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 (0.68), residues: 110
  helix: -1.07 (0.77), residues: 39
  sheet: -1.63 (1.24), residues: 14
  loop : -3.56 (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   0.017   0.003   PHE A  19 
 ARG   0.008   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 fitting.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7626 (mm-30)
  outliers start: 4
  outliers final: 2
  residues processed: 24
  average time/residue: 0.2882
  time to fit residues: 8.5947
Evaluate side-chains
  21 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 18
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 SER
Chi-restraints excluded: chain A residue   68 THR
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 28 optimal weight:    4.9990
   chunk 23 optimal weight:   10.0000
   chunk 9 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   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:    1.9990
   chunk 3 optimal weight:    3.9990
   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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.5331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.063   7440  Z= 0.488
  Angle     :  1.013   7.834  11400  Z= 0.493
  Chirality :  0.051   0.267   1493
  Planarity :  0.008   0.039    435
  Dihedral  : 27.655 172.269   4397
  Min Nonbonded Distance : 1.828

Molprobity Statistics.
  All-atom Clashscore : 35.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.36 %
    Favored  : 83.64 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 18.37 %
    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: -3.50 (0.73), residues: 110
  helix: -1.63 (0.74), residues: 40
  sheet: -1.53 (1.19), residues: 14
  loop : -3.14 (0.79), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP A 108 
 HIS   0.007   0.003   HIS A  43 
 PHE   0.043   0.005   PHE A  19 
 ARG   0.006   0.001   ARG A  10 

*********************** 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
  27 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 21
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.7080 (mtt180)
REVERT: A   31 GLN cc_start: 0.7867 (tp-100) cc_final: 0.7549 (tp40)
  outliers start: 6
  outliers final: 3
  residues processed: 24
  average time/residue: 0.3152
  time to fit residues: 9.2468
Evaluate side-chains
  22 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 18
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ARG
Chi-restraints excluded: chain A residue   15 SER
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   68 THR
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:   10.0000
   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:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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: 0.7734
moved from start:          0.5089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   7440  Z= 0.380
  Angle     :  0.881   7.724  11400  Z= 0.434
  Chirality :  0.046   0.251   1493
  Planarity :  0.007   0.043    435
  Dihedral  : 27.471 172.586   4397
  Min Nonbonded Distance : 1.847

Molprobity Statistics.
  All-atom Clashscore : 30.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.45 %
    Favored  : 84.55 %
  Rotamer:
    Outliers :  7.14 %
    Allowed  : 20.41 %
    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: -3.14 (0.77), residues: 110
  helix: -1.22 (0.80), residues: 40
  sheet: -1.34 (1.18), residues: 14
  loop : -3.02 (0.83), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.002   TRP A 108 
 HIS   0.004   0.002   HIS A  59 
 PHE   0.010   0.002   PHE A  84 
 ARG   0.004   0.001   ARG A  10 

*********************** 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
  28 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 21
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 4
  residues processed: 25
  average time/residue: 0.2133
  time to fit residues: 7.0185
Evaluate side-chains
  22 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 18
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 SER
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   68 THR
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 15 optimal weight:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 7 optimal weight:    0.1980
   chunk 21 optimal weight:    3.9990
   overall best weight:    2.0186

-------------------------------------------------------------------------------
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: 0.7703
moved from start:          0.4931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   7440  Z= 0.307
  Angle     :  0.810   7.273  11400  Z= 0.402
  Chirality :  0.042   0.255   1493
  Planarity :  0.006   0.039    435
  Dihedral  : 27.367 173.306   4397
  Min Nonbonded Distance : 1.877

Molprobity Statistics.
  All-atom Clashscore : 26.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.64 %
    Favored  : 86.36 %
  Rotamer:
    Outliers : 10.20 %
    Allowed  : 20.41 %
    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: -2.90 (0.77), residues: 110
  helix: -0.97 (0.81), residues: 40
  sheet: -1.28 (1.09), residues: 14
  loop : -2.91 (0.83), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP A 108 
 HIS   0.004   0.002   HIS A  43 
 PHE   0.008   0.002   PHE A   5 
 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
  29 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 19
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6995 (mtt180)
REVERT: A   90 LYS cc_start: 0.7754 (tptm) cc_final: 0.7496 (tptp)
  outliers start: 10
  outliers final: 6
  residues processed: 26
  average time/residue: 0.2571
  time to fit residues: 8.4451
Evaluate side-chains
  25 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 18
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ARG
Chi-restraints excluded: chain A residue   15 SER
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   68 THR
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   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:    2.7990

-------------------------------------------------------------------------------
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 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.5407

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= 0.408
  Angle     :  0.927   7.721  11400  Z= 0.456
  Chirality :  0.047   0.271   1493
  Planarity :  0.007   0.053    435
  Dihedral  : 27.547 172.208   4397
  Min Nonbonded Distance : 1.845

Molprobity Statistics.
  All-atom Clashscore : 32.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.18 %
    Favored  : 81.82 %
  Rotamer:
    Outliers :  7.14 %
    Allowed  : 22.45 %
    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: -3.03 (0.77), residues: 110
  helix: -1.03 (0.83), residues: 40
  sheet: -1.73 (1.08), residues: 14
  loop : -2.91 (0.83), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.003   TRP A 108 
 HIS   0.005   0.002   HIS A  59 
 PHE   0.011   0.002   PHE A  19 
 ARG   0.004   0.001   ARG A  61 

*********************** 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
  28 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 21
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7125 (mtt180)
REVERT: A   90 LYS cc_start: 0.7509 (tptm) cc_final: 0.7230 (tptp)
  outliers start: 7
  outliers final: 3
  residues processed: 25
  average time/residue: 0.2829
  time to fit residues: 8.6706
Evaluate side-chains
  23 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ARG
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   68 THR
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:    1.9990
   chunk 23 optimal weight:    9.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    2.9990

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.5724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.058   7440  Z= 0.433
  Angle     :  0.957   7.787  11400  Z= 0.470
  Chirality :  0.049   0.294   1493
  Planarity :  0.007   0.053    435
  Dihedral  : 27.648 172.090   4397
  Min Nonbonded Distance : 1.836

Molprobity Statistics.
  All-atom Clashscore : 31.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.27 %
    Favored  : 82.73 %
  Rotamer:
    Outliers :  8.16 %
    Allowed  : 20.41 %
    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: -3.13 (0.76), residues: 110
  helix: -1.18 (0.81), residues: 40
  sheet: -1.76 (1.06), residues: 14
  loop : -2.91 (0.83), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.005   TRP A 108 
 HIS   0.006   0.002   HIS A  43 
 PHE   0.010   0.002   PHE A  84 
 ARG   0.003   0.001   ARG A  10 

*********************** 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
  30 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 22
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7276 (mtt180)
  outliers start: 8
  outliers final: 6
  residues processed: 26
  average time/residue: 0.4028
  time to fit residues: 12.5409
Evaluate side-chains
  26 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 19
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ARG
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  111 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   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:    0.0980
   overall best weight:    2.4188

-------------------------------------------------------------------------------
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: 0.7734
moved from start:          0.5513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   7440  Z= 0.360
  Angle     :  0.886   9.641  11400  Z= 0.436
  Chirality :  0.045   0.279   1493
  Planarity :  0.007   0.050    435
  Dihedral  : 27.485 173.268   4397
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 29.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.45 %
    Favored  : 84.55 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 26.53 %
    Favored  : 67.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.48 (0.75), residues: 110
  helix: -1.57 (0.76), residues: 46
  sheet: -1.73 (1.00), residues: 14
  loop : -3.23 (0.84), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.004   TRP A 108 
 HIS   0.004   0.002   HIS A  43 
 PHE   0.010   0.002   PHE A  19 
 ARG   0.003   0.001   ARG A  10 

*********************** 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
  27 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 21
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7475 (mtt180)
REVERT: A   90 LYS cc_start: 0.7356 (tppt) cc_final: 0.6820 (tptp)
  outliers start: 6
  outliers final: 5
  residues processed: 24
  average time/residue: 0.2882
  time to fit residues: 8.5715
Evaluate side-chains
  24 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 18
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ARG
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   86 VAL
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 30 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 36 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 23 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   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**
** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.5965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.056   7440  Z= 0.461
  Angle     :  1.010   9.618  11400  Z= 0.493
  Chirality :  0.050   0.288   1493
  Planarity :  0.007   0.058    435
  Dihedral  : 27.742 172.349   4397
  Min Nonbonded Distance : 1.816

Molprobity Statistics.
  All-atom Clashscore : 35.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.00 %
    Favored  : 80.00 %
  Rotamer:
    Outliers :  7.14 %
    Allowed  : 26.53 %
    Favored  : 66.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.72 (0.73), residues: 110
  helix: -1.79 (0.75), residues: 46
  sheet: -1.45 (1.07), residues: 14
  loop : -3.47 (0.81), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.005   TRP A 108 
 HIS   0.006   0.002   HIS A  43 
 PHE   0.013   0.003   PHE A  84 
 ARG   0.004   0.001   ARG A 113 

*********************** 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
  28 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 21
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7216 (mtt180)
REVERT: A   90 LYS cc_start: 0.7411 (tppt) cc_final: 0.6900 (tptp)
  outliers start: 7
  outliers final: 4
  residues processed: 25
  average time/residue: 0.2929
  time to fit residues: 9.0724
Evaluate side-chains
  25 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 20
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ARG
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   85 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 32 optimal weight:    3.9990
   chunk 9 optimal weight:    0.4980
   chunk 27 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
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: 0.7631
moved from start:          0.5078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7440  Z= 0.206
  Angle     :  0.749   8.780  11400  Z= 0.373
  Chirality :  0.037   0.266   1493
  Planarity :  0.005   0.037    435
  Dihedral  : 27.218 175.097   4397
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 21.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.73 %
    Favored  : 87.27 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 30.61 %
    Favored  : 65.31 %
  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: -3.01 (0.77), residues: 110
  helix: -1.10 (0.82), residues: 46
  sheet: -1.48 (1.05), residues: 14
  loop : -3.04 (0.82), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.003   TRP A 108 
 HIS   0.002   0.001   HIS A  43 
 PHE   0.010   0.002   PHE A  19 
 ARG   0.003   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 fitting.
    rotamer outliers: 4
    poor density    : 20
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 LYS cc_start: 0.7170 (tppt) cc_final: 0.6621 (tptp)
  outliers start: 4
  outliers final: 2
  residues processed: 23
  average time/residue: 0.2766
  time to fit residues: 8.0006
Evaluate side-chains
  23 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 21
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   85 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 1 optimal weight:    0.8980
   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:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    3.3788

-------------------------------------------------------------------------------
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  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 = 0.3925 r_free = 0.3925 target = 0.059347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.046028 restraints weight = 56009.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 1.73
r_work: 0.3331 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.5932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.057   7440  Z= 0.482
  Angle     :  1.016   9.077  11400  Z= 0.494
  Chirality :  0.050   0.277   1493
  Planarity :  0.007   0.057    435
  Dihedral  : 27.653 174.023   4397
  Min Nonbonded Distance : 1.816

Molprobity Statistics.
  All-atom Clashscore : 35.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.00 %
    Favored  : 80.00 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 30.61 %
    Favored  : 67.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.44 (0.76), residues: 110
  helix: -1.49 (0.78), residues: 46
  sheet: -1.30 (1.08), residues: 14
  loop : -3.39 (0.83), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.004   TRP A 108 
 HIS   0.005   0.002   HIS A  43 
 PHE   0.012   0.003   PHE A  84 
 ARG   0.005   0.001   ARG A  10 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1498.08 seconds
wall clock time: 28 minutes 3.92 seconds (1683.92 seconds total)