Starting phenix.real_space_refine
on Sun Mar 17 02:43:12 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo1_26637/03_2024/7uo1_26637.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo1_26637/03_2024/7uo1_26637.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo1_26637/03_2024/7uo1_26637.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo1_26637/03_2024/7uo1_26637.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo1_26637/03_2024/7uo1_26637.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo1_26637/03_2024/7uo1_26637.pdb"
  }
  resolution = 3.2
  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
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Ca     10      9.91       5
     P     454      5.49       5
     S       2      5.16       5
     C    4934      2.51       5
     N    1993      2.21       5
     O    3301      1.98       5
     H    5894      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  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: 16588
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 12071
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 373, 12071
          Classifications: {'RNA': 373}
          Modifications used: {'3*END': 1, '5*END': 1, 'rna2p_pur': 25, 'rna2p_pyr': 26, 'rna3p_pur': 191, 'rna3p_pyr': 128}
          Link IDs: {'rna2p': 51, 'rna3p': 321}
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      Number of atoms: 2622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 2622
          Classifications: {'RNA': 82}
          Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 37, 'rna3p_pyr': 36}
          Link IDs: {'rna2p': 8, 'rna3p': 73}
    Chain: "A"
      Number of atoms: 1885
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 1885
          Classifications: {'peptide': 112}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 105}
    Chain: "B"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Unusual residues: {' CA': 10}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
  Residues with excluded nonbonded symmetry interactions: 46
    residue:
      pdb=" P     C B  20 " occ=0.00
      ... (29 atoms not shown)
      pdb=" H6    C B  20 " occ=0.00
    residue:
      pdb=" P     C B  21 " occ=0.00
      ... (29 atoms not shown)
      pdb=" H6    C B  21 " occ=0.00
    residue:
      pdb=" P     G B  22 " occ=0.00
      ... (32 atoms not shown)
      pdb=" H22   G B  22 " occ=0.00
    residue:
      pdb=" P     C B  23 " occ=0.00
      ... (29 atoms not shown)
      pdb=" H6    C B  23 " occ=0.00
    residue:
      pdb=" P     U B  24 " occ=0.00
      ... (28 atoms not shown)
      pdb=" H6    U B  24 " occ=0.00
    residue:
      pdb=" P     U B  25 " occ=0.00
      ... (28 atoms not shown)
      pdb=" H6    U B  25 " occ=0.00
    residue:
      pdb=" P     C B  26 " occ=0.00
      ... (29 atoms not shown)
      pdb=" H6    C B  26 " occ=0.00
    residue:
      pdb=" P     G B  27 " occ=0.00
      ... (32 atoms not shown)
      pdb=" H22   G B  27 " occ=0.00
    residue:
      pdb=" P     U B  28 " occ=0.00
      ... (28 atoms not shown)
      pdb=" H6    U B  28 " occ=0.00
    residue:
      pdb=" P     C B  29 " occ=0.00
      ... (29 atoms not shown)
      pdb=" H6    C B  29 " occ=0.00
    residue:
      pdb=" P     G B  30 " occ=0.00
      ... (32 atoms not shown)
      pdb=" H22   G B  30 " occ=0.00
    residue:
      pdb=" P     U B  31 " occ=0.00
      ... (28 atoms not shown)
      pdb=" H6    U B  31 " occ=0.00
    ... (remaining 34 not shown)
  Time building chain proxies: 7.86, per 1000 atoms: 0.47
  Number of scatterers: 16588
  At special positions: 0
  Unit cell: (99.6826, 116.048, 196.39, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Ca     10     19.99
     S       2     16.00
     P     454     15.00
     O    3301      8.00
     N    1993      7.00
     C    4934      6.00
     H    5894      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        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: 14.41
  Conformation dependent library (CDL) restraints added in 352.5 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
      45.5% alpha, 13.4% beta
      109 base pairs and 164 stacking pairs defined.
    Time for finding SS restraints: 8.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 9
    Processing helix  chain 'A' and resid 12 through 21
      removed outlier: 3.528A  pdb=" N   PHE A  16 " --> pdb=" O   THR A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 74
    Processing helix  chain 'A' and resid 95 through 111
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27

    45 hydrogen bonds defined for protein.
    126 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      294 hydrogen bonds
      544 hydrogen bond angles
      0 basepair planarities
      109 basepair parallelities
      164 stacking parallelities
  Total time for adding SS restraints: 6.23

  Time building geometry restraints manager: 14.86 seconds

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

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

  Histogram of bond angle deviations from ideal:
       18.39 -    41.51: 42
       41.51 -    64.62: 0
       64.62 -    87.74: 0
       87.74 -   110.86: 15953
      110.86 -   133.97: 15790
  Bond angle restraints: 31785
  Sorted by residual:
  angle pdb=" O3'   U B 299 "
        pdb=" P     G B 300 "
        pdb=" OP1   G B 300 "
      ideal   model   delta    sigma   weight residual
     108.00   18.39   89.61 3.00e+00 1.11e-01 8.92e+02
  angle pdb=" O3'   C B   9 "
        pdb=" P     C B  10 "
        pdb=" OP1   C B  10 "
      ideal   model   delta    sigma   weight residual
     108.00   18.82   89.18 3.00e+00 1.11e-01 8.84e+02
  angle pdb=" O3'   A B  13 "
        pdb=" P     C B  14 "
        pdb=" OP1   C B  14 "
      ideal   model   delta    sigma   weight residual
     108.00   18.84   89.16 3.00e+00 1.11e-01 8.83e+02
  angle pdb=" O3'   C C  75 "
        pdb=" P     C C  76 "
        pdb=" OP1   C C  76 "
      ideal   model   delta    sigma   weight residual
     108.00   19.12   88.88 3.00e+00 1.11e-01 8.78e+02
  angle pdb=" O3'   G B  19 "
        pdb=" P     C B  20 "
        pdb=" OP1   C B  20 "
      ideal   model   delta    sigma   weight residual
     108.00   19.22   88.78 3.00e+00 1.11e-01 8.76e+02
  ... (remaining 31780 not shown)

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

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

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

  Histogram of nonbonded interaction distances:
        1.62 -     2.21: 1249
        2.21 -     2.81: 22703
        2.81 -     3.41: 39051
        3.41 -     4.00: 52292
        4.00 -     4.60: 76175
  Nonbonded interactions: 191470
  Sorted by model distance:
  nonbonded pdb=" O6    G B  52 "
            pdb=" H   ARG A   6 "
     model   vdw
     1.615 1.850
  nonbonded pdb="HO2'   C B 138 "
            pdb=" O5'   A B 139 "
     model   vdw
     1.618 1.850
  nonbonded pdb="HO2'   G B  84 "
            pdb=" O5'   C B  85 "
     model   vdw
     1.632 1.850
  nonbonded pdb=" H62   A B  81 "
            pdb=" O2'   G B 280 "
     model   vdw
     1.635 1.850
  nonbonded pdb="HO2'   C B  35 "
            pdb=" OP2   C B  36 "
     model   vdw
     1.638 1.850
  ... (remaining 191465 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.91
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.070
  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:             0.170
  Extract box with map and model:          1.260
  Check model and map are aligned:         0.250
  Set scattering table:                    0.160
  Process input model:                     57.890
  Find NCS groups from input model:        0.180
  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:             0.010
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   62.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5258
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  11867  Z= 0.144
  Angle     :  4.427  89.611  18304  Z= 1.518
  Chirality :  0.099   0.577   2410
  Planarity :  0.003   0.023    619
  Dihedral  : 31.568 179.992   7521
  Min Nonbonded Distance : 1.799

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

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.82), residues: 110
  helix:  2.24 (0.74), residues: 46
  sheet: -1.81 (0.82), residues: 30
  loop : -1.24 (1.17), residues: 34

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

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

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS    1 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Evaluate side-chains
  41 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 LEU cc_start: 0.7949 (mm) cc_final: 0.7599 (mm)
REVERT: A   72 ARG cc_start: 0.6821 (tpt90) cc_final: 0.6203 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.5752
  time to fit residues: 30.1730
Evaluate side-chains
  34 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    0.0020
   chunk 42 optimal weight:    9.9990
   chunk 23 optimal weight:    9.9990
   chunk 14 optimal weight:    9.9990
   chunk 28 optimal weight:   10.0000
   chunk 22 optimal weight:    9.9990
   chunk 43 optimal weight:    9.9990
   chunk 16 optimal weight:   20.0000
   chunk 26 optimal weight:   20.0000
   chunk 32 optimal weight:    8.9990
   chunk 50 optimal weight:    6.9990
   overall best weight:    7.1996

-------------------------------------------------------------------------------
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: 0.6399
moved from start:          0.5326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.038  11867  Z= 0.411
  Angle     :  2.001  32.592  18304  Z= 0.783
  Chirality :  0.240   2.233   2410
  Planarity :  0.007   0.076    619
  Dihedral  : 31.831 179.646   7276
  Min Nonbonded Distance : 1.663

Molprobity Statistics.
  All-atom Clashscore : 33.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 13.27 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.83), residues: 110
  helix:  0.81 (0.72), residues: 46
  sheet: -1.59 (0.80), residues: 30
  loop : -0.36 (1.36), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.004   TRP A 107 
 HIS   0.008   0.003   HIS A  42 
 PHE   0.015   0.004   PHE A  71 
 ARG   0.009   0.001   ARG A   9 

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

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS    1 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Evaluate side-chains
  36 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.6896 (tpt90) cc_final: 0.4656 (tpt90)
  outliers start: 4
  outliers final: 4
  residues processed: 33
  average time/residue: 0.6677
  time to fit residues: 27.4758
Evaluate side-chains
  33 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   95 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 15 optimal weight:   30.0000
   chunk 42 optimal weight:   10.0000
   chunk 34 optimal weight:    7.9990
   chunk 14 optimal weight:    9.9990
   chunk 50 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 45 optimal weight:    0.5980
   chunk 17 optimal weight:    7.9990
   chunk 40 optimal weight:   40.0000
   chunk 38 optimal weight:   10.0000
   overall best weight:    4.9188

-------------------------------------------------------------------------------
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: 0.6484
moved from start:          0.6172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  11867  Z= 0.274
  Angle     :  1.891  30.393  18304  Z= 0.706
  Chirality :  0.233   2.070   2410
  Planarity :  0.006   0.041    619
  Dihedral  : 31.543 178.911   7276
  Min Nonbonded Distance : 1.709

Molprobity Statistics.
  All-atom Clashscore : 23.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 13.27 %
    Favored  : 83.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.86), residues: 110
  helix:  1.86 (0.75), residues: 46
  sheet: -1.28 (0.85), residues: 30
  loop : -0.53 (1.34), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.002   TRP A 107 
 HIS   0.014   0.004   HIS A  58 
 PHE   0.010   0.002   PHE A   4 
 ARG   0.006   0.001   ARG A  97 

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

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS    1 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Evaluate side-chains
  32 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 29
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLN cc_start: 0.7769 (mp10) cc_final: 0.7540 (mp10)
REVERT: A   72 ARG cc_start: 0.6856 (tpt90) cc_final: 0.4631 (tpt90)
REVERT: A   93 ASP cc_start: 0.8334 (p0) cc_final: 0.8098 (p0)
  outliers start: 3
  outliers final: 3
  residues processed: 29
  average time/residue: 0.6577
  time to fit residues: 23.9028
Evaluate side-chains
  32 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 29
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  110 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 26 optimal weight:   20.0000
   chunk 5 optimal weight:   10.0000
   chunk 24 optimal weight:    6.9990
   chunk 34 optimal weight:    9.9990
   chunk 51 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 48 optimal weight:    7.9990
   chunk 14 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    4.9990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6594
moved from start:          0.7473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  11867  Z= 0.305
  Angle     :  1.881  29.323  18304  Z= 0.710
  Chirality :  0.237   2.117   2410
  Planarity :  0.007   0.074    619
  Dihedral  : 31.617 179.947   7276
  Min Nonbonded Distance : 1.723

Molprobity Statistics.
  All-atom Clashscore : 29.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 13.27 %
    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: -0.14 (0.84), residues: 110
  helix:  1.25 (0.73), residues: 46
  sheet: -1.14 (0.90), residues: 30
  loop : -0.76 (1.31), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.003   TRP A 107 
 HIS   0.011   0.003   HIS A  58 
 PHE   0.007   0.002   PHE A   4 
 ARG   0.013   0.001   ARG A  97 

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

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS    1 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Evaluate side-chains
  35 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 29
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.7004 (tpt90) cc_final: 0.4735 (tpt90)
REVERT: A   93 ASP cc_start: 0.8606 (p0) cc_final: 0.8393 (p0)
REVERT: A   99 LEU cc_start: 0.8103 (tt) cc_final: 0.7473 (tp)
  outliers start: 6
  outliers final: 4
  residues processed: 31
  average time/residue: 0.6217
  time to fit residues: 24.7402
Evaluate side-chains
  33 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   73 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 40 optimal weight:   40.0000
   chunk 22 optimal weight:   10.0000
   chunk 46 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 27 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9990
   chunk 13 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 10 optimal weight:    7.9990
   chunk 31 optimal weight:    6.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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: 0.6641
moved from start:          0.8101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  11867  Z= 0.332
  Angle     :  1.890  30.243  18304  Z= 0.710
  Chirality :  0.236   2.075   2410
  Planarity :  0.006   0.056    619
  Dihedral  : 31.661 179.554   7276
  Min Nonbonded Distance : 1.698

Molprobity Statistics.
  All-atom Clashscore : 29.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 16.33 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.85), residues: 110
  helix:  1.29 (0.75), residues: 46
  sheet: -1.15 (0.88), residues: 30
  loop : -1.34 (1.31), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.003   TRP A 107 
 HIS   0.010   0.003   HIS A  58 
 PHE   0.007   0.003   PHE A  83 
 ARG   0.002   0.001   ARG A  44 

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

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS    1 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Evaluate side-chains
  35 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.456 
Fit side-chains
REVERT: A   72 ARG cc_start: 0.6883 (tpt90) cc_final: 0.4655 (tpt90)
REVERT: A   93 ASP cc_start: 0.8693 (p0) cc_final: 0.8227 (p0)
REVERT: A   97 ARG cc_start: 0.7489 (ttp80) cc_final: 0.7163 (ttp80)
  outliers start: 5
  outliers final: 4
  residues processed: 30
  average time/residue: 0.6785
  time to fit residues: 25.7587
Evaluate side-chains
  34 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 30
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   95 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 54 optimal weight:    6.9990
   chunk 44 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 4 optimal weight:   50.0000
   chunk 17 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 39 optimal weight:   20.0000
   overall best weight:    6.9990

-------------------------------------------------------------------------------
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: 0.6701
moved from start:          0.8852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.066  11867  Z= 0.400
  Angle     :  1.916  29.220  18304  Z= 0.729
  Chirality :  0.238   2.071   2410
  Planarity :  0.008   0.068    619
  Dihedral  : 31.755 179.540   7276
  Min Nonbonded Distance : 1.688

Molprobity Statistics.
  All-atom Clashscore : 35.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 16.33 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.83), residues: 110
  helix:  0.57 (0.71), residues: 46
  sheet: -1.30 (0.88), residues: 30
  loop : -1.54 (1.35), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.003   TRP A 107 
 HIS   0.010   0.003   HIS A  58 
 PHE   0.011   0.003   PHE A  71 
 ARG   0.007   0.001   ARG A  36 

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

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS    1 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Evaluate side-chains
  36 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.6971 (tpt90) cc_final: 0.4671 (tpt90)
  outliers start: 6
  outliers final: 6
  residues processed: 31
  average time/residue: 0.6283
  time to fit residues: 24.7991
Evaluate side-chains
  34 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue   95 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 16 optimal weight:   20.0000
   chunk 10 optimal weight:    6.9990
   chunk 34 optimal weight:    8.9990
   chunk 36 optimal weight:    8.9990
   overall best weight:    4.7788

-------------------------------------------------------------------------------
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: 0.6647
moved from start:          0.8775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  11867  Z= 0.281
  Angle     :  1.855  28.308  18304  Z= 0.691
  Chirality :  0.237   2.078   2410
  Planarity :  0.006   0.042    619
  Dihedral  : 31.551 178.799   7276
  Min Nonbonded Distance : 1.730

Molprobity Statistics.
  All-atom Clashscore : 27.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 17.35 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.86), residues: 110
  helix:  1.38 (0.77), residues: 46
  sheet: -1.28 (0.89), residues: 30
  loop : -1.40 (1.31), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 107 
 HIS   0.009   0.002   HIS A  58 
 PHE   0.008   0.002   PHE A  18 
 ARG   0.003   0.001   ARG A  60 

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

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS    1 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Evaluate side-chains
  34 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.6883 (tpt90) cc_final: 0.4673 (tpt90)
  outliers start: 5
  outliers final: 4
  residues processed: 30
  average time/residue: 0.6187
  time to fit residues: 23.5206
Evaluate side-chains
  33 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   95 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 26 optimal weight:   20.0000
   chunk 5 optimal weight:    9.9990
   chunk 42 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 47 optimal weight:    6.9990
   chunk 50 optimal weight:    0.8980
   chunk 30 optimal weight:    6.9990
   chunk 21 optimal weight:   10.0000
   chunk 39 optimal weight:   20.0000
   chunk 15 optimal weight:   30.0000
   overall best weight:    4.1788

-------------------------------------------------------------------------------
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: 0.6638
moved from start:          0.8919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  11867  Z= 0.257
  Angle     :  1.843  28.423  18304  Z= 0.685
  Chirality :  0.237   2.070   2410
  Planarity :  0.006   0.044    619
  Dihedral  : 31.450 178.618   7276
  Min Nonbonded Distance : 1.747

Molprobity Statistics.
  All-atom Clashscore : 26.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  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: -0.18 (0.86), residues: 110
  helix:  1.64 (0.77), residues: 46
  sheet: -1.19 (0.90), residues: 30
  loop : -1.45 (1.26), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 107 
 HIS   0.008   0.002   HIS A  58 
 PHE   0.008   0.002   PHE A  18 
 ARG   0.004   0.001   ARG A  36 

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

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS    1 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Evaluate side-chains
  32 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.6890 (tpt90) cc_final: 0.4652 (tpt90)
  outliers start: 4
  outliers final: 4
  residues processed: 29
  average time/residue: 0.6579
  time to fit residues: 24.0602
Evaluate side-chains
  32 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   95 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 45 optimal weight:    0.3980
   chunk 47 optimal weight:    0.3980
   chunk 50 optimal weight:    0.5980
   chunk 33 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 32 optimal weight:    7.9990
   chunk 25 optimal weight:    9.9990
   chunk 36 optimal weight:    9.9990
   chunk 55 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 44 optimal weight:    9.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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: 0.6476
moved from start:          0.8531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  11867  Z= 0.129
  Angle     :  1.796  27.763  18304  Z= 0.657
  Chirality :  0.239   2.092   2410
  Planarity :  0.005   0.039    619
  Dihedral  : 31.124 179.147   7276
  Min Nonbonded Distance : 1.839

Molprobity Statistics.
  All-atom Clashscore : 19.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 18.37 %
    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:  0.98 (0.89), residues: 110
  helix:  2.81 (0.76), residues: 46
  sheet: -0.97 (0.91), residues: 30
  loop : -0.80 (1.32), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 110 
 PHE   0.012   0.002   PHE A   4 
 ARG   0.003   0.001   ARG A  68 

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

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS    1 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Evaluate side-chains
  30 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.444 
Fit side-chains
REVERT: A   72 ARG cc_start: 0.6795 (tpt90) cc_final: 0.4552 (tpt90)
  outliers start: 3
  outliers final: 3
  residues processed: 27
  average time/residue: 0.6156
  time to fit residues: 21.2270
Evaluate side-chains
  30 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   48 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 4 optimal weight:   50.0000
   chunk 34 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 35 optimal weight:    6.9990
   chunk 47 optimal weight:    7.9990
   chunk 13 optimal weight:   10.0000
   chunk 40 optimal weight:   40.0000
   chunk 6 optimal weight:    4.9990
   chunk 12 optimal weight:    9.9990
   chunk 44 optimal weight:    9.9990
   chunk 18 optimal weight:   10.0000
   overall best weight:    7.9990

-------------------------------------------------------------------------------
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: 0.6719
moved from start:          0.9248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048  11867  Z= 0.430
  Angle     :  1.929  30.111  18304  Z= 0.731
  Chirality :  0.235   2.066   2410
  Planarity :  0.007   0.074    619
  Dihedral  : 31.550 179.525   7276
  Min Nonbonded Distance : 1.674

Molprobity Statistics.
  All-atom Clashscore : 36.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 18.37 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.82), residues: 110
  helix:  0.94 (0.74), residues: 47
  sheet: -1.27 (0.88), residues: 30
  loop : -1.58 (1.24), residues: 33

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.003   TRP A 107 
 HIS   0.012   0.004   HIS A  58 
 PHE   0.012   0.003   PHE A  71 
 ARG   0.009   0.001   ARG A  36 

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

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS    1 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Evaluate side-chains
  32 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.6948 (tpt90) cc_final: 0.4726 (tpt90)
  outliers start: 4
  outliers final: 4
  residues processed: 29
  average time/residue: 0.6272
  time to fit residues: 23.2360
Evaluate side-chains
  32 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   95 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 45 optimal weight:    0.4980
   chunk 5 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 39 optimal weight:   20.0000
   chunk 2 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 29 optimal weight:    9.9990
   chunk 38 optimal weight:   10.0000
   chunk 1 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    3.4988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4665 r_free = 0.4665 target = 0.239544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.198562 restraints weight = 39484.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.4211 rms_B_bonded: 0.82
r_work: 0.4094 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.4094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6502
moved from start:          0.9116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  11867  Z= 0.226
  Angle     :  1.834  28.371  18304  Z= 0.680
  Chirality :  0.237   2.068   2410
  Planarity :  0.005   0.040    619
  Dihedral  : 31.398 179.190   7276
  Min Nonbonded Distance : 1.766

Molprobity Statistics.
  All-atom Clashscore : 24.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 19.39 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.85), residues: 110
  helix:  1.99 (0.79), residues: 46
  sheet: -1.15 (0.88), residues: 30
  loop : -1.31 (1.19), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP A 107 
 HIS   0.007   0.002   HIS A  58 
 PHE   0.010   0.002   PHE A  18 
 ARG   0.004   0.001   ARG A  97 

===============================================================================
Job complete
usr+sys time: 5095.98 seconds
wall clock time: 90 minutes 15.90 seconds (5415.90 seconds total)