Starting phenix.real_space_refine
on Fri Mar 15 04:48:17 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo0_26636/03_2024/7uo0_26636.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo0_26636/03_2024/7uo0_26636.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo0_26636/03_2024/7uo0_26636.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo0_26636/03_2024/7uo0_26636.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo0_26636/03_2024/7uo0_26636.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo0_26636/03_2024/7uo0_26636.pdb"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

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

  Symmetric amino acids flipped
    Residue "A PHE    5": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 10697
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 922
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 922
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 6, 'TRANS': 105}
    Chain: "B"
      Number of atoms: 8024
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 373, 8024
          Classifications: {'RNA': 373}
          Modifications used: {'5*END': 1, 'rna2p_pur': 27, 'rna2p_pyr': 26, 'rna3p_pur': 191, 'rna3p_pyr': 128}
          Link IDs: {'rna2p': 53, 'rna3p': 319}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 1744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 1744
          Classifications: {'RNA': 82}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 8, 'rna3p_pur': 37, 'rna3p_pyr': 33}
          Link IDs: {'rna2p': 11, 'rna3p': 70}
    Chain: "B"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Unusual residues: {' CA': 7}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
  Residues with excluded nonbonded symmetry interactions: 47
    residue:
      pdb=" P     C B  20 " occ=0.00
      ... (18 atoms not shown)
      pdb=" C6    C B  20 " occ=0.00
    residue:
      pdb=" P     C B  21 " occ=0.00
      ... (18 atoms not shown)
      pdb=" C6    C B  21 " occ=0.00
    residue:
      pdb=" P     G B  22 " occ=0.00
      ... (21 atoms not shown)
      pdb=" C4    G B  22 " occ=0.00
    residue:
      pdb=" P     C B  23 " occ=0.00
      ... (18 atoms not shown)
      pdb=" C6    C B  23 " occ=0.00
    residue:
      pdb=" P     U B  24 " occ=0.00
      ... (18 atoms not shown)
      pdb=" C6    U B  24 " occ=0.00
    residue:
      pdb=" P     U B  25 " occ=0.00
      ... (18 atoms not shown)
      pdb=" C6    U B  25 " occ=0.00
    residue:
      pdb=" P     C B  26 " occ=0.00
      ... (18 atoms not shown)
      pdb=" C6    C B  26 " occ=0.00
    residue:
      pdb=" P     G B  27 " occ=0.00
      ... (21 atoms not shown)
      pdb=" C4    G B  27 " occ=0.00
    residue:
      pdb=" P     U B  28 " occ=0.00
      ... (18 atoms not shown)
      pdb=" C6    U B  28 " occ=0.00
    residue:
      pdb=" P     C B  29 " occ=0.00
      ... (18 atoms not shown)
      pdb=" C6    C B  29 " occ=0.00
    residue:
      pdb=" P     G B  30 " occ=0.00
      ... (21 atoms not shown)
      pdb=" C4    G B  30 " occ=0.00
    residue:
      pdb=" P     U B  31 " occ=0.00
      ... (18 atoms not shown)
      pdb=" C6    U B  31 " occ=0.00
    ... (remaining 35 not shown)
  Time building chain proxies: 6.72, per 1000 atoms: 0.63
  Number of scatterers: 10697
  At special positions: 0
  Unit cell: (125.902, 115.322, 194.672, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      7     19.99
     S       2     16.00
     P     454     15.00
     O    3303      8.00
     N    1996      7.00
     C    4935      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        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: 5.70
  Conformation dependent library (CDL) restraints added in 479.5 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
      40.2% alpha, 11.6% beta
      113 base pairs and 83 stacking pairs defined.
    Time for finding SS restraints: 4.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 10
    Processing helix  chain 'A' and resid 13 through 23
      removed outlier: 3.778A  pdb=" N   PHE A  17 " --> pdb=" O   THR A  13 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   GLN A  23 " --> pdb=" O   PHE A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 75
    Processing helix  chain 'A' and resid 96 through 109
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28
      removed outlier: 3.739A  pdb=" N   GLY A  36 " --> pdb=" O   GLN A  25 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA A  27 " --> pdb=" O   ILE A  34 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 8.903A  pdb=" N   ALA A  88 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)

    34 hydrogen bonds defined for protein.
    93 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      312 hydrogen bonds
      598 hydrogen bond angles
      0 basepair planarities
      113 basepair parallelities
      83 stacking parallelities
  Total time for adding SS restraints: 3.26

  Time building geometry restraints manager: 6.13 seconds

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

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

  Histogram of bond angle deviations from ideal:
       30.65 -    51.54: 5
       51.54 -    72.43: 0
       72.43 -    93.31: 0
       93.31 -   114.20: 10229
      114.20 -   135.09: 8085
  Bond angle restraints: 18319
  Sorted by residual:
  angle pdb=" O3'   C B  14 "
        pdb=" P     A B  15 "
        pdb=" OP1   A B  15 "
      ideal   model   delta    sigma   weight residual
     108.00   30.65   77.35 3.00e+00 1.11e-01 6.65e+02
  angle pdb=" O3'   A B  15 "
        pdb=" P     G B  16 "
        pdb=" OP1   G B  16 "
      ideal   model   delta    sigma   weight residual
     108.00   34.51   73.49 3.00e+00 1.11e-01 6.00e+02
  angle pdb=" O3'   A B 130 "
        pdb=" P     C B 131 "
        pdb=" OP1   C B 131 "
      ideal   model   delta    sigma   weight residual
     108.00   34.71   73.29 3.00e+00 1.11e-01 5.97e+02
  angle pdb=" O3'   C B  70 "
        pdb=" P     C B  71 "
        pdb=" OP1   C B  71 "
      ideal   model   delta    sigma   weight residual
     108.00   35.06   72.94 3.00e+00 1.11e-01 5.91e+02
  angle pdb=" O3'   C B 252 "
        pdb=" P     C B 253 "
        pdb=" OP1   C B 253 "
      ideal   model   delta    sigma   weight residual
     108.00   36.18   71.82 3.00e+00 1.11e-01 5.73e+02
  ... (remaining 18314 not shown)

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

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

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

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 640
        2.67 -     3.23: 8176
        3.23 -     3.79: 17008
        3.79 -     4.34: 18215
        4.34 -     4.90: 27169
  Nonbonded interactions: 71208
  Sorted by model distance:
  nonbonded pdb=" O4    U B  97 "
            pdb=" N6    A B  99 "
     model   vdw
     2.117 2.520
  nonbonded pdb=" O4    U B  25 "
            pdb=" O6    G B  56 "
     model   vdw
     2.129 2.432
  nonbonded pdb=" O2'   G B 291 "
            pdb=" OP2   G B 293 "
     model   vdw
     2.139 2.440
  nonbonded pdb=" O2'   A B 248 "
            pdb=" O2'   A C  74 "
     model   vdw
     2.186 2.440
  nonbonded pdb=" O2'   U B 366 "
            pdb=" O5'   C B 367 "
     model   vdw
     2.207 2.440
  ... (remaining 71203 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             2.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          10.060
  Check model and map are aligned:         0.170
  Set scattering table:                    0.110
  Process input model:                     34.530
  Find NCS groups from input model:        0.180
  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:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3191
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  11874  Z= 0.176
  Angle     :  2.227  77.348  18319  Z= 0.847
  Chirality :  0.111   0.901   2412
  Planarity :  0.004   0.029    619
  Dihedral  : 29.933 179.431   7531
  Min Nonbonded Distance : 2.117

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

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

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

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

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 21
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.6386 (mmt) cc_final: 0.5867 (tpp)
  outliers start: 2
  outliers final: 0
  residues processed: 22
  average time/residue: 0.2942
  time to fit residues: 8.8851
Evaluate side-chains
  11 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 14 optimal weight:    9.9990
   chunk 28 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 26 optimal weight:   10.0000
   chunk 32 optimal weight:    4.9990
   chunk 50 optimal weight:    8.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
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: 0.4587
moved from start:          1.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.073  11874  Z= 0.619
  Angle     :  1.688  12.625  18319  Z= 0.805
  Chirality :  0.074   0.455   2412
  Planarity :  0.013   0.195    619
  Dihedral  : 31.472 179.643   7286
  Min Nonbonded Distance : 1.825

Molprobity Statistics.
  All-atom Clashscore : 43.37
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  :  6.36 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  8.16 %
    Allowed  : 15.31 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.36 (0.75), residues: 110
  helix: -1.39 (0.69), residues: 42
  sheet: -1.51 (1.05), residues: 26
  loop : -1.51 (0.95), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.004   TRP A 108 
 HIS   0.018   0.009   HIS A  43 
 PHE   0.026   0.006   PHE A  19 
 ARG   0.015   0.002   ARG A  73 

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

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 21
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.6499 (OUTLIER) cc_final: 0.6252 (tpp)
  outliers start: 8
  outliers final: 3
  residues processed: 27
  average time/residue: 0.3856
  time to fit residues: 13.1353
Evaluate side-chains
  19 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 15
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   82 MET
Chi-restraints excluded: chain A residue  107 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 15 optimal weight:   10.0000
   chunk 42 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 14 optimal weight:   10.0000
   chunk 50 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    2.3386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4602
moved from start:          1.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  11874  Z= 0.299
  Angle     :  0.999   9.482  18319  Z= 0.479
  Chirality :  0.045   0.243   2412
  Planarity :  0.007   0.081    619
  Dihedral  : 30.776 179.398   7286
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 23.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.91 %
    Favored  : 89.09 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 27.55 %
    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: -2.01 (0.79), residues: 110
  helix: -0.80 (0.80), residues: 40
  sheet: -1.31 (0.94), residues: 30
  loop : -1.67 (1.00), residues: 40

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.004   TRP A 108 
 HIS   0.007   0.002   HIS A  59 
 PHE   0.056   0.006   PHE A  19 
 ARG   0.008   0.001   ARG A  57 

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

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 19
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.6361 (mmt) cc_final: 0.5810 (tpp)
  outliers start: 3
  outliers final: 0
  residues processed: 21
  average time/residue: 0.3693
  time to fit residues: 10.1040
Evaluate side-chains
  16 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   chunk 24 optimal weight:    7.9990
   chunk 34 optimal weight:    5.9990
   chunk 51 optimal weight:   20.0000
   chunk 54 optimal weight:    9.9990
   chunk 48 optimal weight:    4.9990
   chunk 14 optimal weight:    9.9990
   chunk 45 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
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: 0.5061
moved from start:          1.7834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.111  11874  Z= 0.535
  Angle     :  1.414  11.366  18319  Z= 0.679
  Chirality :  0.063   0.302   2412
  Planarity :  0.010   0.083    619
  Dihedral  : 31.788 179.038   7286
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 44.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.73 %
    Favored  : 87.27 %
  Rotamer:
    Outliers :  8.16 %
    Allowed  : 21.43 %
    Favored  : 70.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.76 (0.78), residues: 110
  helix: -1.27 (0.78), residues: 39
  sheet: -1.37 (1.02), residues: 31
  loop : -2.59 (0.91), residues: 40

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 108 
 HIS   0.008   0.003   HIS A  59 
 PHE   0.032   0.006   PHE A  72 
 ARG   0.024   0.002   ARG A  73 

*********************** 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
  27 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 19
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.7722 (tp30) cc_final: 0.7366 (tp30)
REVERT: A  106 LYS cc_start: 0.9378 (mtmm) cc_final: 0.9164 (ptpp)
REVERT: A  109 ARG cc_start: 0.7953 (mmp-170) cc_final: 0.7705 (tpp-160)
  outliers start: 8
  outliers final: 4
  residues processed: 25
  average time/residue: 0.3527
  time to fit residues: 11.4507
Evaluate side-chains
  20 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 16
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   79 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 22 optimal weight:    8.9990
   chunk 46 optimal weight:    0.7980
   chunk 37 optimal weight:   10.0000
   chunk 0 optimal weight:    0.5980
   chunk 27 optimal weight:    8.9990
   chunk 48 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   overall best weight:    1.6784

-------------------------------------------------------------------------------
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: 0.4897
moved from start:          1.7490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11874  Z= 0.231
  Angle     :  0.865  10.707  18319  Z= 0.420
  Chirality :  0.042   0.238   2412
  Planarity :  0.006   0.045    619
  Dihedral  : 30.877 178.306   7286
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 20.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  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: -2.59 (0.74), residues: 110
  helix: -0.92 (0.77), residues: 40
  sheet: -1.95 (0.85), residues: 30
  loop : -2.12 (0.94), residues: 40

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 108 
 HIS   0.009   0.002   HIS A  59 
 PHE   0.046   0.005   PHE A  19 
 ARG   0.004   0.001   ARG A  56 

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

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 18
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.5987 (mtt) cc_final: 0.5758 (mtm)
  outliers start: 7
  outliers final: 2
  residues processed: 24
  average time/residue: 0.2887
  time to fit residues: 9.4397
Evaluate side-chains
  18 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 16
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue  101 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 54 optimal weight:    8.9990
   chunk 44 optimal weight:    3.9990
   chunk 25 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 52 optimal weight:   30.0000
   chunk 6 optimal weight:    0.5980
   chunk 30 optimal weight:    3.9990
   chunk 39 optimal weight:    8.9990
   overall best weight:    2.9188

-------------------------------------------------------------------------------
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: 0.5123
moved from start:          1.9640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.085  11874  Z= 0.392
  Angle     :  1.112  10.905  18319  Z= 0.536
  Chirality :  0.052   0.416   2412
  Planarity :  0.008   0.074    619
  Dihedral  : 31.358 176.176   7286
  Min Nonbonded Distance : 1.848

Molprobity Statistics.
  All-atom Clashscore : 32.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.91 %
    Favored  : 89.09 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 27.55 %
    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: -3.18 (0.75), residues: 110
  helix: -2.00 (0.72), residues: 41
  sheet: -1.56 (0.92), residues: 31
  loop : -2.41 (0.97), residues: 38

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 108 
 HIS   0.003   0.001   HIS A  77 
 PHE   0.016   0.003   PHE A  17 
 ARG   0.005   0.001   ARG A 109 

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

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 17
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 HIS cc_start: 0.7213 (OUTLIER) cc_final: 0.7012 (p90)
  outliers start: 5
  outliers final: 2
  residues processed: 22
  average time/residue: 0.3226
  time to fit residues: 9.5785
Evaluate side-chains
  19 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 16
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  108 TRP
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:    4.9990
   chunk 53 optimal weight:    8.9990
   chunk 33 optimal weight:    7.9990
   chunk 32 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 10 optimal weight:    0.6980
   chunk 34 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    3.9388

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5271
moved from start:          2.1965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.086  11874  Z= 0.471
  Angle     :  1.259  13.982  18319  Z= 0.594
  Chirality :  0.057   0.327   2412
  Planarity :  0.008   0.068    619
  Dihedral  : 31.632 178.733   7286
  Min Nonbonded Distance : 1.787

Molprobity Statistics.
  All-atom Clashscore : 42.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.91 %
    Favored  : 89.09 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 29.59 %
    Favored  : 68.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.12 (0.69), residues: 110
  helix: -2.71 (0.65), residues: 40
  sheet: -2.48 (0.78), residues: 31
  loop : -2.59 (0.97), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP A 108 
 HIS   0.008   0.003   HIS A  59 
 PHE   0.019   0.004   PHE A  19 
 ARG   0.010   0.002   ARG A  73 

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

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 17
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.5984 (mtt) cc_final: 0.5688 (mtm)
REVERT: A  105 GLU cc_start: 0.8584 (tp30) cc_final: 0.8362 (tp30)
REVERT: A  110 ARG cc_start: 0.8649 (ptt90) cc_final: 0.8189 (mmm160)
  outliers start: 2
  outliers final: 0
  residues processed: 19
  average time/residue: 0.4045
  time to fit residues: 9.8342
Evaluate side-chains
  17 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 5 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 49 optimal weight:   10.0000
   chunk 51 optimal weight:   20.0000
   chunk 47 optimal weight:    4.9990
   chunk 50 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 15 optimal weight:   10.0000
   overall best weight:    3.9788

-------------------------------------------------------------------------------
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: 0.5329
moved from start:          2.3450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.096  11874  Z= 0.463
  Angle     :  1.236  12.813  18319  Z= 0.580
  Chirality :  0.056   0.345   2412
  Planarity :  0.008   0.050    619
  Dihedral  : 31.635 179.375   7286
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 43.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.91 %
    Favored  : 89.09 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 25.51 %
    Favored  : 68.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.49 (0.77), residues: 110
  helix: -2.43 (0.66), residues: 40
  sheet: -2.06 (0.78), residues: 31
  loop : -2.03 (1.20), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.004   TRP A 108 
 HIS   0.005   0.003   HIS A  77 
 PHE   0.021   0.003   PHE A  19 
 ARG   0.007   0.002   ARG A  61 

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

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 20
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 HIS cc_start: 0.6895 (OUTLIER) cc_final: 0.6488 (p90)
REVERT: A  110 ARG cc_start: 0.8595 (ptt90) cc_final: 0.8036 (mmm160)
  outliers start: 6
  outliers final: 4
  residues processed: 25
  average time/residue: 0.3791
  time to fit residues: 12.3204
Evaluate side-chains
  21 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 16
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue   73 ARG
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  108 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 50 optimal weight:    9.9990
   chunk 33 optimal weight:    7.9990
   chunk 53 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 51 optimal weight:   20.0000
   chunk 44 optimal weight:    2.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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: 0.5393
moved from start:          2.4459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.094  11874  Z= 0.506
  Angle     :  1.263  13.682  18319  Z= 0.595
  Chirality :  0.057   0.348   2412
  Planarity :  0.009   0.083    619
  Dihedral  : 31.747 179.833   7286
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 46.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.73 %
    Favored  : 87.27 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 26.53 %
    Favored  : 69.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.97 (0.71), residues: 110
  helix: -2.70 (0.65), residues: 40
  sheet: -2.38 (0.76), residues: 31
  loop : -2.40 (1.06), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 108 
 HIS   0.005   0.003   HIS A  77 
 PHE   0.013   0.003   PHE A  72 
 ARG   0.009   0.001   ARG A  66 

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

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 17
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 HIS cc_start: 0.6783 (OUTLIER) cc_final: 0.6331 (p90)
REVERT: A  110 ARG cc_start: 0.8655 (ptt90) cc_final: 0.8192 (mmm160)
  outliers start: 4
  outliers final: 3
  residues processed: 20
  average time/residue: 0.4297
  time to fit residues: 10.8912
Evaluate side-chains
  21 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 17
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue   73 ARG
Chi-restraints excluded: chain A residue  108 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 4 optimal weight:    0.1980
   chunk 34 optimal weight:    5.9990
   chunk 27 optimal weight:    9.9990
   chunk 35 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 6 optimal weight:    0.4980
   chunk 12 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
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: 0.5247
moved from start:          2.4036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  11874  Z= 0.249
  Angle     :  0.905  11.315  18319  Z= 0.429
  Chirality :  0.041   0.245   2412
  Planarity :  0.007   0.087    619
  Dihedral  : 31.101 179.928   7286
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 23.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 29.59 %
    Favored  : 68.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.02 (0.76), residues: 110
  helix: -1.78 (0.68), residues: 41
  sheet: -2.47 (0.68), residues: 31
  loop : -1.39 (1.23), residues: 38

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 108 
 HIS   0.004   0.001   HIS A  59 
 PHE   0.010   0.002   PHE A  19 
 ARG   0.004   0.001   ARG A  66 

********************** 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
  19 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 17
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 HIS cc_start: 0.6494 (OUTLIER) cc_final: 0.6149 (p90)
REVERT: A   90 LYS cc_start: 0.8873 (tppt) cc_final: 0.8601 (mmmt)
  outliers start: 2
  outliers final: 0
  residues processed: 19
  average time/residue: 0.3461
  time to fit residues: 8.7620
Evaluate side-chains
  18 residues out of total 98 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 17
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 5 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 39 optimal weight:   10.0000
   chunk 2 optimal weight:    0.6980
   chunk 32 optimal weight:    5.9990
   chunk 50 optimal weight:   10.0000
   chunk 29 optimal weight:    7.9990
   chunk 38 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   overall best weight:    1.8584

-------------------------------------------------------------------------------
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 = 0.4392 r_free = 0.4392 target = 0.112798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.100352 restraints weight = 84402.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.4065 rms_B_bonded: 1.37
r_work (final): 0.4065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6080
moved from start:          2.4296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  11874  Z= 0.270
  Angle     :  0.891  11.442  18319  Z= 0.428
  Chirality :  0.041   0.240   2412
  Planarity :  0.006   0.059    619
  Dihedral  : 31.031 179.906   7286
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 25.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 31.63 %
    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: -3.30 (0.74), residues: 110
  helix: -1.83 (0.70), residues: 41
  sheet: -2.75 (0.64), residues: 31
  loop : -1.66 (1.17), residues: 38

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 108 
 HIS   0.004   0.002   HIS A  59 
 PHE   0.013   0.003   PHE A  19 
 ARG   0.009   0.001   ARG A  73 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1781.82 seconds
wall clock time: 33 minutes 6.55 seconds (1986.55 seconds total)