Starting phenix.real_space_refine
on Wed Sep 17 05:12:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vie_65085/09_2025/9vie_65085.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vie_65085/09_2025/9vie_65085.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.38
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vie_65085/09_2025/9vie_65085.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vie_65085/09_2025/9vie_65085.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vie_65085/09_2025/9vie_65085.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vie_65085/09_2025/9vie_65085.cif"
  }
  resolution = 2.38
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.057
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: 5
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     S      26      5.16       5
     C    3074      2.51       5
     N     830      2.21       5
     O     812      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4746
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1109
          Classifications: {'peptide': 141}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 134}
    Chain: "B"
      Number of atoms: 1174
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1174
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 142}
    Chain: "A"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'CMO': 1, 'HEM': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'CMO': 1, 'HEM': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    C, D
  Time building chain proxies: 1.36, per 1000 atoms: 0.29
  Number of scatterers: 4746
  At special positions: 0
  Unit cell: (74.46, 82.62, 65.28, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      4     26.01
     S      26     16.00
     O     812      8.00
     N     830      7.00
     C    3074      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.48
  Conformation dependent library (CDL) restraints added in 179.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1104

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 0 sheets defined
      82.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 15
    Processing helix  chain 'A' and resid 20 through 36
    Processing helix  chain 'A' and resid 37 through 43
    Processing helix  chain 'A' and resid 52 through 72
    Processing helix  chain 'A' and resid 75 through 80
    Processing helix  chain 'A' and resid 80 through 89
    Processing helix  chain 'A' and resid 94 through 113
      removed outlier: 4.245A  pdb=" N   PHE A  98 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   LYS A  99 " --> pdb=" O   PRO A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 136
    Processing helix  chain 'B' and resid 4 through 16
      removed outlier: 3.584A  pdb=" N   ALA B  16 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 35
    Processing helix  chain 'B' and resid 36 through 46
      removed outlier: 4.025A  pdb=" N   GLU B  43 " --> pdb=" O   ARG B  40 " (cutoff:3.500A)
      removed outlier: 5.772A  pdb=" N   HIS B  44 " --> pdb=" O   TYR B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 57
    Processing helix  chain 'B' and resid 57 through 72
    Processing helix  chain 'B' and resid 73 through 77
    Processing helix  chain 'B' and resid 80 through 85
    Processing helix  chain 'B' and resid 85 through 95
    Processing helix  chain 'B' and resid 101 through 118
      removed outlier: 4.168A  pdb=" N   LEU B 105 " --> pdb=" O   GLU B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 142
    Processing helix  chain 'C' and resid 3 through 15
    Processing helix  chain 'C' and resid 20 through 36
    Processing helix  chain 'C' and resid 37 through 43
    Processing helix  chain 'C' and resid 52 through 72
    Processing helix  chain 'C' and resid 75 through 80
    Processing helix  chain 'C' and resid 80 through 89
    Processing helix  chain 'C' and resid 94 through 113
      removed outlier: 4.245A  pdb=" N   PHE C  98 " --> pdb=" O   ASP C  94 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   LYS C  99 " --> pdb=" O   PRO C  95 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 136
    Processing helix  chain 'D' and resid 4 through 16
      removed outlier: 3.584A  pdb=" N   ALA D  16 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 19 through 35
    Processing helix  chain 'D' and resid 36 through 46
      removed outlier: 4.025A  pdb=" N   GLU D  43 " --> pdb=" O   ARG D  40 " (cutoff:3.500A)
      removed outlier: 5.772A  pdb=" N   HIS D  44 " --> pdb=" O   TYR D  41 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 57
    Processing helix  chain 'D' and resid 57 through 72
    Processing helix  chain 'D' and resid 73 through 77
    Processing helix  chain 'D' and resid 80 through 85
    Processing helix  chain 'D' and resid 85 through 95
    Processing helix  chain 'D' and resid 101 through 118
      removed outlier: 4.168A  pdb=" N   LEU D 105 " --> pdb=" O   GLU D 101 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 123 through 142

    326 hydrogen bonds defined for protein.
    906 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.76

  Time building geometry restraints manager: 0.57 seconds

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

  Histogram of bond lengths:
        1.20 -     1.38: 1870
        1.38 -     1.57: 2972
        1.57 -     1.75: 2
        1.75 -     1.93: 38
        1.93 -     2.12: 14
  Bond restraints: 4896
  Sorted by residual:
  bond pdb=" C3B HEM A 201 "
       pdb=" CAB HEM A 201 "
    ideal  model  delta    sigma   weight residual
    1.544  1.431  0.113 2.00e-02 2.50e+03 3.22e+01
  bond pdb=" C3B HEM C 201 "
       pdb=" CAB HEM C 201 "
    ideal  model  delta    sigma   weight residual
    1.544  1.431  0.113 2.00e-02 2.50e+03 3.22e+01
  bond pdb=" C3B HEM B 201 "
       pdb=" CAB HEM B 201 "
    ideal  model  delta    sigma   weight residual
    1.544  1.468  0.076 2.00e-02 2.50e+03 1.43e+01
  bond pdb=" C3B HEM D 201 "
       pdb=" CAB HEM D 201 "
    ideal  model  delta    sigma   weight residual
    1.544  1.468  0.076 2.00e-02 2.50e+03 1.43e+01
  bond pdb=" C2A HEM A 201 "
       pdb=" CAA HEM A 201 "
    ideal  model  delta    sigma   weight residual
    1.544  1.469  0.075 2.00e-02 2.50e+03 1.40e+01
  ... (remaining 4891 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 5296
        1.86 -     3.71: 1120
        3.71 -     5.57: 202
        5.57 -     7.43: 46
        7.43 -     9.28: 6
  Bond angle restraints: 6670
  Sorted by residual:
  angle pdb=" CA  ASP B   4 "
        pdb=" CB  ASP B   4 "
        pdb=" CG  ASP B   4 "
      ideal   model   delta    sigma   weight residual
     112.60  118.94   -6.34 1.00e+00 1.00e+00 4.02e+01
  angle pdb=" CA  ASP D   4 "
        pdb=" CB  ASP D   4 "
        pdb=" CG  ASP D   4 "
      ideal   model   delta    sigma   weight residual
     112.60  118.94   -6.34 1.00e+00 1.00e+00 4.02e+01
  angle pdb=" CA  HIS C  87 "
        pdb=" CB  HIS C  87 "
        pdb=" CG  HIS C  87 "
      ideal   model   delta    sigma   weight residual
     113.80  107.83    5.97 1.00e+00 1.00e+00 3.57e+01
  angle pdb=" CA  HIS A  87 "
        pdb=" CB  HIS A  87 "
        pdb=" CG  HIS A  87 "
      ideal   model   delta    sigma   weight residual
     113.80  107.83    5.97 1.00e+00 1.00e+00 3.57e+01
  angle pdb=" CA  ASP D  19 "
        pdb=" CB  ASP D  19 "
        pdb=" CG  ASP D  19 "
      ideal   model   delta    sigma   weight residual
     112.60  118.25   -5.65 1.00e+00 1.00e+00 3.19e+01
  ... (remaining 6665 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.93: 2512
       17.93 -    35.85: 210
       35.85 -    53.78: 40
       53.78 -    71.70: 22
       71.70 -    89.62: 18
  Dihedral angle restraints: 2802
    sinusoidal: 1114
      harmonic: 1688
  Sorted by residual:
  dihedral pdb=" CD  ARG A  92 "
           pdb=" NE  ARG A  92 "
           pdb=" CZ  ARG A  92 "
           pdb=" NH1 ARG A  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -33.09   33.09     1      1.00e+01 1.00e-02 1.56e+01
  dihedral pdb=" CD  ARG C  92 "
           pdb=" NE  ARG C  92 "
           pdb=" CZ  ARG C  92 "
           pdb=" NH1 ARG C  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -33.09   33.09     1      1.00e+01 1.00e-02 1.56e+01
  dihedral pdb=" CA  THR C 137 "
           pdb=" C   THR C 137 "
           pdb=" N   SER C 138 "
           pdb=" CA  SER C 138 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.31  -19.69     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 2799 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 350
       0.055 -    0.110: 196
       0.110 -    0.165: 86
       0.165 -    0.219: 42
       0.219 -    0.274: 12
  Chirality restraints: 686
  Sorted by residual:
  chirality pdb=" CA  PRO D 100 "
            pdb=" N   PRO D 100 "
            pdb=" C   PRO D 100 "
            pdb=" CB  PRO D 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.44    0.27 2.00e-01 2.50e+01 1.88e+00
  chirality pdb=" CA  PRO B 100 "
            pdb=" N   PRO B 100 "
            pdb=" C   PRO B 100 "
            pdb=" CB  PRO B 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.44    0.27 2.00e-01 2.50e+01 1.88e+00
  chirality pdb=" CB  ILE A  73 "
            pdb=" CA  ILE A  73 "
            pdb=" CG1 ILE A  73 "
            pdb=" CG2 ILE A  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.87e+00
  ... (remaining 683 not shown)

  Planarity restraints: 836
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  14 "    0.118 2.00e-02 2.50e+03   5.59e-02 7.82e+01
        pdb=" CG  TRP A  14 "   -0.064 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  14 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  14 "   -0.029 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  14 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  14 "    0.026 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  14 "   -0.061 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  14 "    0.029 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  14 "   -0.034 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  14 "    0.065 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C  14 "   -0.118 2.00e-02 2.50e+03   5.59e-02 7.82e+01
        pdb=" CG  TRP C  14 "    0.064 2.00e-02 2.50e+03
        pdb=" CD1 TRP C  14 "    0.043 2.00e-02 2.50e+03
        pdb=" CD2 TRP C  14 "    0.029 2.00e-02 2.50e+03
        pdb=" NE1 TRP C  14 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TRP C  14 "   -0.026 2.00e-02 2.50e+03
        pdb=" CE3 TRP C  14 "    0.061 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C  14 "   -0.029 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C  14 "    0.034 2.00e-02 2.50e+03
        pdb=" CH2 TRP C  14 "   -0.065 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  41 "    0.099 2.00e-02 2.50e+03   5.12e-02 5.23e+01
        pdb=" CG  TYR D  41 "   -0.072 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  41 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  41 "   -0.036 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  41 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  41 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  41 "   -0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR D  41 "    0.061 2.00e-02 2.50e+03
  ... (remaining 833 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.97: 1942
        2.97 -     3.70: 8362
        3.70 -     4.42: 14932
        4.42 -     5.14: 23512
        5.14 -     5.86: 28022
  Nonbonded interactions: 76770
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B  99 "
            pdb=" OH  TYR C  42 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OH  TYR A  42 "
            pdb=" OD2 ASP D  99 "
     model   vdw
     2.252 3.040
  nonbonded pdb="FE   HEM C 201 "
            pdb=" C   CMO C 202 "
     model   vdw
     2.336 3.910
  nonbonded pdb="FE   HEM A 201 "
            pdb=" C   CMO A 202 "
     model   vdw
     2.336 3.910
  nonbonded pdb=" OG  SER B  89 "
            pdb=" O   LEU B 141 "
     model   vdw
     2.463 3.040
  ... (remaining 76765 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.710
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.000
  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:6.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
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      :  0.014   0.205   4900  Z= 0.764
  Angle     :  1.635   9.283   6670  Z= 1.068
  Chirality :  0.089   0.274    686
  Planarity :  0.022   0.285    836
  Dihedral  : 16.944  89.625   1698
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  :  2.08 %
    Favored  : 95.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.60 (0.31), residues: 566
  helix: -1.33 (0.21), residues: 416
  sheet:  None (None), residues: 0
  loop :  0.48 (0.53), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.034   0.008   ARG B  40 
 TYR   0.099   0.015   TYR D  41 
 PHE   0.043   0.011   PHE B 130 
 TRP   0.118   0.024   TRP A  14 
 HIS   0.020   0.005   HIS D 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.01376 ( 4896)
  covalent geometry    : angle       1.63542 ( 6670)
  hydrogen bonds       : bond        0.22591 (  326)
  hydrogen bonds       : angle       6.72029 (  906)
  Misc. bond           : bond        0.14901 (    4)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A    4 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6869 (mmp)
REVERT: A    5 GLU cc_start: 0.7008 (tp30) cc_final: 0.6103 (tm-30)
REVERT: A   11 LYS cc_start: 0.7669 (mttt) cc_final: 0.7294 (mttp)
REVERT: A   92 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6977 (mmt180)
REVERT: A   99 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7859 (mtmt)
REVERT: A  120 GLU cc_start: 0.7769 (mt-10) cc_final: 0.6967 (mp0)
REVERT: B   13 ASP cc_start: 0.8461 (m-30) cc_final: 0.8232 (m-30)
REVERT: B   40 ARG cc_start: 0.6560 (OUTLIER) cc_final: 0.6320 (ptm160)
REVERT: B   59 LYS cc_start: 0.7882 (mttt) cc_final: 0.7463 (mtpt)
REVERT: B   76 LYS cc_start: 0.7623 (mtpt) cc_final: 0.7090 (mptp)
REVERT: B   94 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7928 (mt-10)
REVERT: B  101 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8228 (mm-30)
REVERT: B  104 LYS cc_start: 0.8049 (mtmt) cc_final: 0.7419 (mtmm)
REVERT: B  120 GLU cc_start: 0.7694 (mt-10) cc_final: 0.6975 (mp0)
REVERT: B  125 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7176 (mp0)
REVERT: C    4 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.6867 (mmp)
REVERT: C    5 GLU cc_start: 0.7004 (tp30) cc_final: 0.6099 (tm-30)
REVERT: C   11 LYS cc_start: 0.7667 (mttt) cc_final: 0.7293 (mttp)
REVERT: C   92 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6976 (mmt180)
REVERT: C   99 LYS cc_start: 0.8128 (mtmt) cc_final: 0.7860 (mtmt)
REVERT: C  120 GLU cc_start: 0.7769 (mt-10) cc_final: 0.6966 (mp0)
REVERT: D   13 ASP cc_start: 0.8460 (m-30) cc_final: 0.8232 (m-30)
REVERT: D   40 ARG cc_start: 0.6559 (OUTLIER) cc_final: 0.6318 (ptm160)
REVERT: D   59 LYS cc_start: 0.7883 (mttt) cc_final: 0.7463 (mtpt)
REVERT: D   76 LYS cc_start: 0.7624 (mtpt) cc_final: 0.7090 (mptp)
REVERT: D   94 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7927 (mt-10)
REVERT: D  101 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8229 (mm-30)
REVERT: D  104 LYS cc_start: 0.8048 (mtmt) cc_final: 0.7419 (mtmm)
REVERT: D  120 GLU cc_start: 0.7695 (mt-10) cc_final: 0.6977 (mp0)
REVERT: D  125 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7178 (mp0)
  outliers start: 14
  outliers final: 2
  residues processed: 124
  average time/residue: 0.9446
  time to fit residues: 119.8781
Evaluate side-chains
  110 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 102
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 MET
Chi-restraints excluded: chain A residue   18 SER
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   40 ARG
Chi-restraints excluded: chain C residue    4 MET
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain D residue   40 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0070
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
B  52 HIS
B  87 ASN
B 102 ASN
C  50 HIS
C  58 HIS
D  52 HIS
D  87 ASN
D 102 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.142819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.118108 restraints weight = 4000.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 1.39
r_work: 0.3139 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   4900  Z= 0.125
  Angle     :  0.611   8.412   6670  Z= 0.286
  Chirality :  0.040   0.129    686
  Planarity :  0.004   0.044    836
  Dihedral  : 11.886  80.824    664
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  :  6.46 %
    Favored  : 91.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.34), residues: 566
  helix:  1.48 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  1.20 (0.54), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  31 
 TYR   0.012   0.001   TYR D  41 
 PHE   0.013   0.001   PHE B 130 
 TRP   0.015   0.002   TRP C  14 
 HIS   0.004   0.001   HIS C 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 4896)
  covalent geometry    : angle       0.61093 ( 6670)
  hydrogen bonds       : bond        0.04331 (  326)
  hydrogen bonds       : angle       4.06840 (  906)
  Misc. bond           : bond        0.06651 (    4)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7865 (mttt) cc_final: 0.7436 (mttp)
REVERT: A   85 GLU cc_start: 0.6564 (pt0) cc_final: 0.5805 (pp20)
REVERT: A   99 LYS cc_start: 0.8425 (mtmt) cc_final: 0.8135 (mtmt)
REVERT: B    6 HIS cc_start: 0.7860 (m170) cc_final: 0.7484 (m-70)
REVERT: B   13 ASP cc_start: 0.8741 (m-30) cc_final: 0.8370 (m-30)
REVERT: B   47 LYS cc_start: 0.7630 (mtpp) cc_final: 0.6048 (pmtt)
REVERT: B   59 LYS cc_start: 0.8154 (mttt) cc_final: 0.7731 (mtpt)
REVERT: B   76 LYS cc_start: 0.7868 (mtpt) cc_final: 0.7523 (mptp)
REVERT: B   87 ASN cc_start: 0.8529 (m-40) cc_final: 0.8101 (m110)
REVERT: B   90 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7140 (pttm)
REVERT: B  104 LYS cc_start: 0.8385 (mtmt) cc_final: 0.7830 (mtmm)
REVERT: B  120 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7420 (mp0)
REVERT: B  125 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7865 (mp0)
REVERT: C   11 LYS cc_start: 0.7864 (mttt) cc_final: 0.7432 (mttp)
REVERT: C   85 GLU cc_start: 0.6552 (pt0) cc_final: 0.5791 (pp20)
REVERT: C   99 LYS cc_start: 0.8433 (mtmt) cc_final: 0.8147 (mtmt)
REVERT: D    6 HIS cc_start: 0.7868 (m170) cc_final: 0.7490 (m-70)
REVERT: D   13 ASP cc_start: 0.8744 (m-30) cc_final: 0.8372 (m-30)
REVERT: D   47 LYS cc_start: 0.7625 (mtpp) cc_final: 0.6039 (pmtt)
REVERT: D   59 LYS cc_start: 0.8145 (mttt) cc_final: 0.7721 (mtpt)
REVERT: D   76 LYS cc_start: 0.7872 (mtpt) cc_final: 0.7531 (mptp)
REVERT: D   87 ASN cc_start: 0.8522 (m-40) cc_final: 0.8094 (m110)
REVERT: D   90 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7133 (pttm)
REVERT: D  104 LYS cc_start: 0.8378 (mtmt) cc_final: 0.7826 (mtmm)
REVERT: D  120 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7428 (mp0)
REVERT: D  125 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7876 (mp0)
  outliers start: 11
  outliers final: 2
  residues processed: 123
  average time/residue: 0.8608
  time to fit residues: 108.5441
Evaluate side-chains
  112 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 108
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain B residue   90 LYS
Chi-restraints excluded: chain C residue   61 LYS
Chi-restraints excluded: chain D residue   90 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 11 optimal weight:    0.2980
   chunk 7 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 29 optimal weight:    0.3980
   chunk 33 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 39 optimal weight:    0.1980
   chunk 36 optimal weight:   10.0000
   chunk 34 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A  71 ASN
B  56 HIS
B  61 GLN
B 117 HIS
C  71 ASN
D  56 HIS
D  61 GLN
D 117 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.144592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.120605 restraints weight = 4013.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 1.37
r_work: 0.3171 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.084   4900  Z= 0.114
  Angle     :  0.558   5.321   6670  Z= 0.262
  Chirality :  0.039   0.117    686
  Planarity :  0.004   0.047    836
  Dihedral  :  9.506  83.858    640
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 11.25 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.90 (0.35), residues: 566
  helix:  2.23 (0.25), residues: 410
  sheet:  None (None), residues: 0
  loop :  1.27 (0.55), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  31 
 TYR   0.010   0.001   TYR B  41 
 PHE   0.010   0.001   PHE A  63 
 TRP   0.011   0.002   TRP A  14 
 HIS   0.004   0.001   HIS C 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 4896)
  covalent geometry    : angle       0.55843 ( 6670)
  hydrogen bonds       : bond        0.03846 (  326)
  hydrogen bonds       : angle       3.86794 (  906)
  Misc. bond           : bond        0.07945 (    4)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 102
  time to evaluate  : 0.196 
Fit side-chains
REVERT: A    4 MET cc_start: 0.7424 (mmm) cc_final: 0.6908 (mmp)
REVERT: A    5 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6236 (tm-30)
REVERT: A   11 LYS cc_start: 0.7824 (mttt) cc_final: 0.7467 (mttp)
REVERT: A   51 ASN cc_start: 0.7938 (OUTLIER) cc_final: 0.7709 (m110)
REVERT: A   85 GLU cc_start: 0.6535 (pt0) cc_final: 0.5795 (pp20)
REVERT: A   99 LYS cc_start: 0.8456 (mtmt) cc_final: 0.8173 (mtmt)
REVERT: A  127 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7680 (mtmm)
REVERT: B    6 HIS cc_start: 0.7791 (m170) cc_final: 0.7458 (m-70)
REVERT: B   59 LYS cc_start: 0.8092 (mttt) cc_final: 0.7749 (mtpt)
REVERT: B   62 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7716 (mm-30)
REVERT: B   76 LYS cc_start: 0.7859 (mtpt) cc_final: 0.7568 (mmtm)
REVERT: B  120 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7455 (mp0)
REVERT: B  125 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7645 (mp0)
REVERT: C    4 MET cc_start: 0.7418 (mmm) cc_final: 0.6903 (mmp)
REVERT: C    5 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6233 (tm-30)
REVERT: C   11 LYS cc_start: 0.7823 (mttt) cc_final: 0.7463 (mttp)
REVERT: C   85 GLU cc_start: 0.6537 (pt0) cc_final: 0.5790 (pp20)
REVERT: C   99 LYS cc_start: 0.8457 (mtmt) cc_final: 0.8176 (mtmt)
REVERT: C  127 LYS cc_start: 0.8111 (mtmt) cc_final: 0.7672 (mtmm)
REVERT: D    6 HIS cc_start: 0.7793 (m170) cc_final: 0.7453 (m-70)
REVERT: D   59 LYS cc_start: 0.8084 (mttt) cc_final: 0.7742 (mtpt)
REVERT: D   62 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7716 (mm-30)
REVERT: D   76 LYS cc_start: 0.7865 (mtpt) cc_final: 0.7576 (mmtm)
REVERT: D  120 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7460 (mp0)
REVERT: D  125 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7640 (mp0)
  outliers start: 6
  outliers final: 0
  residues processed: 104
  average time/residue: 0.8590
  time to fit residues: 91.6757
Evaluate side-chains
  103 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 100
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 GLU
Chi-restraints excluded: chain A residue   51 ASN
Chi-restraints excluded: chain C residue    5 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 1 optimal weight:    0.0370
   chunk 17 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.7458

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

Flipped N/Q/H residues before XYZ refinement:
A  71 ASN
B  61 GLN
B  87 ASN
C  71 ASN
D  61 GLN
D  87 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.142858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.119055 restraints weight = 4020.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 1.35
r_work: 0.3152 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.111   4900  Z= 0.129
  Angle     :  0.569   5.325   6670  Z= 0.271
  Chirality :  0.040   0.120    686
  Planarity :  0.004   0.049    836
  Dihedral  :  9.199  81.467    640
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.67 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.04 (0.36), residues: 566
  helix:  2.36 (0.25), residues: 410
  sheet:  None (None), residues: 0
  loop :  1.25 (0.56), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  31 
 TYR   0.010   0.001   TYR B  41 
 PHE   0.009   0.001   PHE C  63 
 TRP   0.011   0.002   TRP A  14 
 HIS   0.005   0.001   HIS A 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 4896)
  covalent geometry    : angle       0.56917 ( 6670)
  hydrogen bonds       : bond        0.04233 (  326)
  hydrogen bonds       : angle       3.90621 (  906)
  Misc. bond           : bond        0.08943 (    4)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.196 
Fit side-chains
REVERT: A    5 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6249 (tm-30)
REVERT: A   11 LYS cc_start: 0.7795 (mttt) cc_final: 0.7423 (mttp)
REVERT: A   51 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7644 (m110)
REVERT: A   85 GLU cc_start: 0.6547 (pt0) cc_final: 0.5808 (pp20)
REVERT: A   99 LYS cc_start: 0.8483 (mtmt) cc_final: 0.8179 (mtmt)
REVERT: A  127 LYS cc_start: 0.8182 (mtmt) cc_final: 0.7734 (mtmm)
REVERT: B    6 HIS cc_start: 0.7806 (m170) cc_final: 0.7482 (m-70)
REVERT: B    8 ARG cc_start: 0.7836 (ttm170) cc_final: 0.7403 (mtt-85)
REVERT: B   59 LYS cc_start: 0.8206 (mttt) cc_final: 0.7797 (mtpt)
REVERT: B   62 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7768 (mm-30)
REVERT: B   76 LYS cc_start: 0.7860 (mtpt) cc_final: 0.7612 (mmtm)
REVERT: B  120 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7387 (mp0)
REVERT: B  125 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7930 (mp0)
REVERT: C    5 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6241 (tm-30)
REVERT: C   11 LYS cc_start: 0.7794 (mttt) cc_final: 0.7421 (mttp)
REVERT: C   85 GLU cc_start: 0.6555 (pt0) cc_final: 0.5808 (pp20)
REVERT: C   99 LYS cc_start: 0.8486 (mtmt) cc_final: 0.8183 (mtmt)
REVERT: C  127 LYS cc_start: 0.8180 (mtmt) cc_final: 0.7733 (mtmm)
REVERT: D    6 HIS cc_start: 0.7795 (m170) cc_final: 0.7473 (m-70)
REVERT: D    8 ARG cc_start: 0.7837 (ttm170) cc_final: 0.7402 (mtt-85)
REVERT: D   59 LYS cc_start: 0.8204 (mttt) cc_final: 0.7794 (mtpt)
REVERT: D   62 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7769 (mm-30)
REVERT: D   76 LYS cc_start: 0.7859 (mtpt) cc_final: 0.7614 (mmtm)
REVERT: D  120 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7395 (mp0)
REVERT: D  125 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7919 (mp0)
  outliers start: 8
  outliers final: 2
  residues processed: 104
  average time/residue: 0.8482
  time to fit residues: 90.5349
Evaluate side-chains
  103 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 GLU
Chi-restraints excluded: chain A residue   51 ASN
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain C residue    5 GLU
Chi-restraints excluded: chain C residue   81 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  71 ASN
B  61 GLN
B  87 ASN
C  71 ASN
D  61 GLN
D  87 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.142115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.118317 restraints weight = 4031.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 1.36
r_work: 0.3141 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.112   4900  Z= 0.135
  Angle     :  0.571   5.472   6670  Z= 0.274
  Chirality :  0.041   0.120    686
  Planarity :  0.004   0.050    836
  Dihedral  :  9.236  81.817    640
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 11.46 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.07 (0.36), residues: 566
  helix:  2.35 (0.25), residues: 410
  sheet:  None (None), residues: 0
  loop :  1.35 (0.57), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  31 
 TYR   0.011   0.002   TYR D  41 
 PHE   0.008   0.001   PHE C  63 
 TRP   0.010   0.002   TRP A  14 
 HIS   0.005   0.001   HIS C 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 4896)
  covalent geometry    : angle       0.57122 ( 6670)
  hydrogen bonds       : bond        0.04386 (  326)
  hydrogen bonds       : angle       3.92599 (  906)
  Misc. bond           : bond        0.08666 (    4)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7836 (mttt) cc_final: 0.7456 (mttp)
REVERT: A   85 GLU cc_start: 0.6639 (pt0) cc_final: 0.5902 (pp20)
REVERT: A   99 LYS cc_start: 0.8477 (mtmt) cc_final: 0.8183 (mtmt)
REVERT: A  127 LYS cc_start: 0.8243 (mtmt) cc_final: 0.7803 (mtmm)
REVERT: B    6 HIS cc_start: 0.7850 (m170) cc_final: 0.7533 (m-70)
REVERT: B    8 ARG cc_start: 0.7851 (ttm170) cc_final: 0.7425 (mtt-85)
REVERT: B   59 LYS cc_start: 0.8187 (mttt) cc_final: 0.7834 (mtpt)
REVERT: B   62 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7779 (mm-30)
REVERT: B   76 LYS cc_start: 0.7857 (mtpt) cc_final: 0.7656 (mmtm)
REVERT: B  125 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7648 (mp0)
REVERT: C   11 LYS cc_start: 0.7836 (mttt) cc_final: 0.7454 (mttp)
REVERT: C   85 GLU cc_start: 0.6646 (pt0) cc_final: 0.5899 (pp20)
REVERT: C   99 LYS cc_start: 0.8478 (mtmt) cc_final: 0.8184 (mtmt)
REVERT: C  127 LYS cc_start: 0.8245 (mtmt) cc_final: 0.7803 (mtmm)
REVERT: D    6 HIS cc_start: 0.7852 (m170) cc_final: 0.7530 (m-70)
REVERT: D    8 ARG cc_start: 0.7850 (ttm170) cc_final: 0.7422 (mtt-85)
REVERT: D   59 LYS cc_start: 0.8181 (mttt) cc_final: 0.7829 (mtpt)
REVERT: D   62 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7777 (mm-30)
REVERT: D   76 LYS cc_start: 0.7853 (mtpt) cc_final: 0.7652 (mmtm)
REVERT: D  120 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7405 (mp0)
REVERT: D  125 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7643 (mp0)
  outliers start: 5
  outliers final: 2
  residues processed: 103
  average time/residue: 0.8789
  time to fit residues: 92.8489
Evaluate side-chains
  100 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 98
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain C residue   81 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0570
   chunk 6 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   overall best weight:    0.9500

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

Flipped N/Q/H residues before XYZ refinement:
A  71 ASN
B  61 GLN
B  87 ASN
C  71 ASN
D  61 GLN
D  87 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.142180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.117740 restraints weight = 4057.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 1.39
r_work: 0.3133 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.118   4900  Z= 0.142
  Angle     :  0.580   5.393   6670  Z= 0.279
  Chirality :  0.041   0.121    686
  Planarity :  0.004   0.050    836
  Dihedral  :  9.277  81.941    640
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 12.08 %
    Favored  : 86.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.04 (0.36), residues: 566
  helix:  2.32 (0.25), residues: 410
  sheet:  None (None), residues: 0
  loop :  1.38 (0.57), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  31 
 TYR   0.011   0.002   TYR B  41 
 PHE   0.007   0.001   PHE B 130 
 TRP   0.010   0.002   TRP A  14 
 HIS   0.005   0.001   HIS A 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 4896)
  covalent geometry    : angle       0.58039 ( 6670)
  hydrogen bonds       : bond        0.04538 (  326)
  hydrogen bonds       : angle       3.94644 (  906)
  Misc. bond           : bond        0.09194 (    4)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7849 (mttt) cc_final: 0.7463 (mttp)
REVERT: A   85 GLU cc_start: 0.6702 (pt0) cc_final: 0.5899 (tp30)
REVERT: A   99 LYS cc_start: 0.8424 (mtmt) cc_final: 0.8123 (mtmt)
REVERT: A  127 LYS cc_start: 0.8238 (mtmt) cc_final: 0.7771 (mtmm)
REVERT: B    6 HIS cc_start: 0.7850 (m170) cc_final: 0.7500 (m-70)
REVERT: B    8 ARG cc_start: 0.7847 (ttm170) cc_final: 0.7426 (mtt-85)
REVERT: B   59 LYS cc_start: 0.8136 (mttt) cc_final: 0.7764 (mtpt)
REVERT: B   62 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7720 (mm-30)
REVERT: B   76 LYS cc_start: 0.7819 (mtpt) cc_final: 0.7600 (mmtm)
REVERT: B   94 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7411 (mt-10)
REVERT: B  125 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7612 (mp0)
REVERT: C   11 LYS cc_start: 0.7849 (mttt) cc_final: 0.7461 (mttp)
REVERT: C   85 GLU cc_start: 0.6702 (pt0) cc_final: 0.5885 (tp30)
REVERT: C   99 LYS cc_start: 0.8428 (mtmt) cc_final: 0.8128 (mtmt)
REVERT: C  127 LYS cc_start: 0.8241 (mtmt) cc_final: 0.7776 (mtmm)
REVERT: D    6 HIS cc_start: 0.7831 (m170) cc_final: 0.7488 (m-70)
REVERT: D    8 ARG cc_start: 0.7851 (ttm170) cc_final: 0.7427 (mtt-85)
REVERT: D   59 LYS cc_start: 0.8135 (mttt) cc_final: 0.7761 (mtpt)
REVERT: D   62 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7736 (mm-30)
REVERT: D   76 LYS cc_start: 0.7817 (mtpt) cc_final: 0.7602 (mmtm)
REVERT: D   94 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7410 (mt-10)
REVERT: D  120 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7388 (mp0)
REVERT: D  125 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7592 (mp0)
  outliers start: 5
  outliers final: 2
  residues processed: 101
  average time/residue: 0.8790
  time to fit residues: 91.0203
Evaluate side-chains
  100 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 98
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain C residue   81 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  71 ASN
B  61 GLN
B  87 ASN
C  71 ASN
D  61 GLN
D  87 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.142380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.118095 restraints weight = 3985.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 1.38
r_work: 0.3139 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.2634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.114   4900  Z= 0.135
  Angle     :  0.572   5.299   6670  Z= 0.273
  Chirality :  0.041   0.119    686
  Planarity :  0.004   0.050    836
  Dihedral  :  9.242  82.191    640
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 11.67 %
    Favored  : 87.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.06 (0.36), residues: 566
  helix:  2.35 (0.25), residues: 410
  sheet:  None (None), residues: 0
  loop :  1.33 (0.58), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  31 
 TYR   0.010   0.001   TYR D  41 
 PHE   0.008   0.001   PHE A  63 
 TRP   0.011   0.002   TRP A  14 
 HIS   0.005   0.001   HIS A 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 4896)
  covalent geometry    : angle       0.57207 ( 6670)
  hydrogen bonds       : bond        0.04344 (  326)
  hydrogen bonds       : angle       3.92542 (  906)
  Misc. bond           : bond        0.08922 (    4)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.191 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7815 (mttt) cc_final: 0.7423 (mttp)
REVERT: A   51 ASN cc_start: 0.7969 (OUTLIER) cc_final: 0.7623 (m110)
REVERT: A   85 GLU cc_start: 0.6642 (pt0) cc_final: 0.5913 (pp20)
REVERT: A   99 LYS cc_start: 0.8402 (mtmt) cc_final: 0.8097 (mtmt)
REVERT: A  127 LYS cc_start: 0.8206 (mtmt) cc_final: 0.7737 (mtmm)
REVERT: B    6 HIS cc_start: 0.7865 (m170) cc_final: 0.7519 (m-70)
REVERT: B    8 ARG cc_start: 0.7835 (ttm170) cc_final: 0.7395 (mtt-85)
REVERT: B   59 LYS cc_start: 0.8089 (mttt) cc_final: 0.7712 (mtpt)
REVERT: B   76 LYS cc_start: 0.7799 (mtpt) cc_final: 0.7575 (mmtm)
REVERT: B  125 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7595 (mp0)
REVERT: C   11 LYS cc_start: 0.7810 (mttt) cc_final: 0.7417 (mttp)
REVERT: C   85 GLU cc_start: 0.6632 (pt0) cc_final: 0.5895 (pp20)
REVERT: C   99 LYS cc_start: 0.8401 (mtmt) cc_final: 0.8096 (mtmt)
REVERT: C  127 LYS cc_start: 0.8216 (mtmt) cc_final: 0.7750 (mtmm)
REVERT: D    6 HIS cc_start: 0.7804 (m170) cc_final: 0.7470 (m-70)
REVERT: D    8 ARG cc_start: 0.7843 (ttm170) cc_final: 0.7403 (mtt-85)
REVERT: D   59 LYS cc_start: 0.8089 (mttt) cc_final: 0.7710 (mtpt)
REVERT: D   76 LYS cc_start: 0.7801 (mtpt) cc_final: 0.7581 (mmtm)
REVERT: D  120 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7362 (mp0)
REVERT: D  125 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7568 (mp0)
  outliers start: 5
  outliers final: 2
  residues processed: 101
  average time/residue: 0.8754
  time to fit residues: 90.7257
Evaluate side-chains
  101 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ASN
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain C residue   81 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A  71 ASN
B  61 GLN
B  87 ASN
C  71 ASN
D  61 GLN
D  87 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.142750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.118346 restraints weight = 4049.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 1.39
r_work: 0.3139 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.2655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.110   4900  Z= 0.133
  Angle     :  0.571   5.302   6670  Z= 0.272
  Chirality :  0.040   0.118    686
  Planarity :  0.004   0.050    836
  Dihedral  :  9.229  82.256    640
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 11.67 %
    Favored  : 87.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.10 (0.36), residues: 566
  helix:  2.38 (0.25), residues: 410
  sheet:  None (None), residues: 0
  loop :  1.33 (0.57), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  31 
 TYR   0.010   0.001   TYR D  41 
 PHE   0.008   0.001   PHE C  63 
 TRP   0.011   0.002   TRP A  14 
 HIS   0.004   0.001   HIS A 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 4896)
  covalent geometry    : angle       0.57134 ( 6670)
  hydrogen bonds       : bond        0.04296 (  326)
  hydrogen bonds       : angle       3.91348 (  906)
  Misc. bond           : bond        0.08711 (    4)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7758 (mttt) cc_final: 0.7360 (mttp)
REVERT: A   51 ASN cc_start: 0.7970 (OUTLIER) cc_final: 0.7624 (m110)
REVERT: A   85 GLU cc_start: 0.6669 (pt0) cc_final: 0.5863 (tp30)
REVERT: A   99 LYS cc_start: 0.8411 (mtmt) cc_final: 0.8106 (mtmt)
REVERT: A  127 LYS cc_start: 0.8218 (mtmt) cc_final: 0.7750 (mtmm)
REVERT: B    6 HIS cc_start: 0.7907 (m170) cc_final: 0.7545 (m-70)
REVERT: B    8 ARG cc_start: 0.7843 (ttm170) cc_final: 0.7405 (mtt-85)
REVERT: B   59 LYS cc_start: 0.8107 (mttt) cc_final: 0.7730 (mtpt)
REVERT: B   76 LYS cc_start: 0.7805 (mtpt) cc_final: 0.7584 (mmtm)
REVERT: B  125 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7537 (mp0)
REVERT: C   11 LYS cc_start: 0.7750 (mttt) cc_final: 0.7351 (mttp)
REVERT: C   85 GLU cc_start: 0.6657 (pt0) cc_final: 0.5844 (tp30)
REVERT: C   99 LYS cc_start: 0.8416 (mtmt) cc_final: 0.8109 (mtmt)
REVERT: C  127 LYS cc_start: 0.8228 (mtmt) cc_final: 0.7764 (mtmm)
REVERT: D    6 HIS cc_start: 0.7896 (m170) cc_final: 0.7540 (m-70)
REVERT: D    8 ARG cc_start: 0.7855 (ttm170) cc_final: 0.7418 (mtt-85)
REVERT: D   59 LYS cc_start: 0.8109 (mttt) cc_final: 0.7731 (mtpt)
REVERT: D   76 LYS cc_start: 0.7808 (mtpt) cc_final: 0.7593 (mmtm)
REVERT: D  120 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7380 (mp0)
REVERT: D  125 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7512 (mp0)
  outliers start: 5
  outliers final: 2
  residues processed: 101
  average time/residue: 0.8759
  time to fit residues: 90.7132
Evaluate side-chains
  101 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ASN
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain C residue   81 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  71 ASN
B  61 GLN
B  87 ASN
C  71 ASN
D  61 GLN
D  87 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.142718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.118360 restraints weight = 4004.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 1.38
r_work: 0.3140 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.106   4900  Z= 0.134
  Angle     :  0.576   5.333   6670  Z= 0.274
  Chirality :  0.040   0.118    686
  Planarity :  0.004   0.050    836
  Dihedral  :  9.234  82.245    640
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 12.08 %
    Favored  : 86.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.08 (0.36), residues: 566
  helix:  2.37 (0.25), residues: 410
  sheet:  None (None), residues: 0
  loop :  1.32 (0.57), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  31 
 TYR   0.010   0.001   TYR D  41 
 PHE   0.008   0.001   PHE B 130 
 TRP   0.011   0.002   TRP A  14 
 HIS   0.005   0.001   HIS A 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 4896)
  covalent geometry    : angle       0.57551 ( 6670)
  hydrogen bonds       : bond        0.04328 (  326)
  hydrogen bonds       : angle       3.91871 (  906)
  Misc. bond           : bond        0.08465 (    4)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7757 (mttt) cc_final: 0.7359 (mttp)
REVERT: A   51 ASN cc_start: 0.7991 (OUTLIER) cc_final: 0.7647 (m110)
REVERT: A   85 GLU cc_start: 0.6624 (pt0) cc_final: 0.5864 (tp30)
REVERT: A   99 LYS cc_start: 0.8414 (mtmt) cc_final: 0.8110 (mtmt)
REVERT: A  127 LYS cc_start: 0.8230 (mtmt) cc_final: 0.7760 (mtmm)
REVERT: B    6 HIS cc_start: 0.7913 (m170) cc_final: 0.7545 (m-70)
REVERT: B    8 ARG cc_start: 0.7845 (ttm170) cc_final: 0.7408 (mtt-85)
REVERT: B   59 LYS cc_start: 0.8114 (mttt) cc_final: 0.7737 (mtpt)
REVERT: B   76 LYS cc_start: 0.7808 (mtpt) cc_final: 0.7590 (mmtm)
REVERT: B  125 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7538 (mp0)
REVERT: C   11 LYS cc_start: 0.7757 (mttt) cc_final: 0.7359 (mttp)
REVERT: C   85 GLU cc_start: 0.6619 (pt0) cc_final: 0.5847 (tp30)
REVERT: C   99 LYS cc_start: 0.8418 (mtmt) cc_final: 0.8113 (mtmt)
REVERT: C  127 LYS cc_start: 0.8241 (mtmt) cc_final: 0.7774 (mtmm)
REVERT: D    6 HIS cc_start: 0.7900 (m170) cc_final: 0.7544 (m-70)
REVERT: D    8 ARG cc_start: 0.7858 (ttm170) cc_final: 0.7421 (mtt-85)
REVERT: D   59 LYS cc_start: 0.8111 (mttt) cc_final: 0.7733 (mtpt)
REVERT: D   76 LYS cc_start: 0.7812 (mtpt) cc_final: 0.7598 (mmtm)
REVERT: D  120 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7386 (mp0)
REVERT: D  125 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7520 (mp0)
  outliers start: 5
  outliers final: 2
  residues processed: 101
  average time/residue: 0.8850
  time to fit residues: 91.6761
Evaluate side-chains
  101 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ASN
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain C residue   81 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    0.3980
   chunk 14 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0070
   chunk 36 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.4998

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

Flipped N/Q/H residues before XYZ refinement:
A  71 ASN
B  61 GLN
B  87 ASN
C  71 ASN
D  61 GLN
D  87 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.145069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.120814 restraints weight = 3985.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 1.38
r_work: 0.3172 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.2795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   4900  Z= 0.110
  Angle     :  0.544   5.164   6670  Z= 0.253
  Chirality :  0.038   0.113    686
  Planarity :  0.004   0.050    836
  Dihedral  :  9.111  82.682    640
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 11.67 %
    Favored  : 87.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.31 (0.36), residues: 566
  helix:  2.56 (0.25), residues: 410
  sheet:  None (None), residues: 0
  loop :  1.35 (0.58), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  31 
 TYR   0.007   0.001   TYR D  41 
 PHE   0.009   0.001   PHE A  63 
 TRP   0.010   0.002   TRP A  14 
 HIS   0.004   0.001   HIS C 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 4896)
  covalent geometry    : angle       0.54382 ( 6670)
  hydrogen bonds       : bond        0.03593 (  326)
  hydrogen bonds       : angle       3.80138 (  906)
  Misc. bond           : bond        0.06162 (    4)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7749 (mttt) cc_final: 0.7274 (mttp)
REVERT: A   51 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7687 (m110)
REVERT: A   85 GLU cc_start: 0.6684 (pt0) cc_final: 0.5945 (pp20)
REVERT: A   99 LYS cc_start: 0.8388 (mtmt) cc_final: 0.8073 (mtmt)
REVERT: A  127 LYS cc_start: 0.8188 (mtmt) cc_final: 0.7728 (mtmm)
REVERT: B    6 HIS cc_start: 0.7807 (m170) cc_final: 0.7471 (m-70)
REVERT: B    8 ARG cc_start: 0.7845 (ttm170) cc_final: 0.7408 (mtt-85)
REVERT: B   59 LYS cc_start: 0.8093 (mttt) cc_final: 0.7715 (mtpt)
REVERT: B  125 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7555 (mp0)
REVERT: C   11 LYS cc_start: 0.7752 (mttt) cc_final: 0.7277 (mttp)
REVERT: C   85 GLU cc_start: 0.6685 (pt0) cc_final: 0.5938 (pp20)
REVERT: C   99 LYS cc_start: 0.8383 (mtmt) cc_final: 0.8066 (mtmt)
REVERT: C  127 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7743 (mtmm)
REVERT: D    6 HIS cc_start: 0.7795 (m170) cc_final: 0.7466 (m-70)
REVERT: D    8 ARG cc_start: 0.7850 (ttm170) cc_final: 0.7414 (mtt-85)
REVERT: D   59 LYS cc_start: 0.8084 (mttt) cc_final: 0.7704 (mtpt)
REVERT: D  120 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7327 (mp0)
REVERT: D  125 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7532 (mp0)
  outliers start: 5
  outliers final: 2
  residues processed: 101
  average time/residue: 0.8746
  time to fit residues: 90.6490
Evaluate side-chains
  99 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 96
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ASN
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain C residue   81 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0980
   chunk 18 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 8 optimal weight:    0.2980
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
A  71 ASN
B  61 GLN
B  87 ASN
C  71 ASN
D  61 GLN
D  87 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.144320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.120017 restraints weight = 4016.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.39
r_work: 0.3163 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080   4900  Z= 0.117
  Angle     :  0.555   5.283   6670  Z= 0.260
  Chirality :  0.039   0.113    686
  Planarity :  0.004   0.049    836
  Dihedral  :  9.133  82.683    640
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 11.04 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.27 (0.36), residues: 566
  helix:  2.54 (0.25), residues: 410
  sheet:  None (None), residues: 0
  loop :  1.27 (0.57), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  31 
 TYR   0.008   0.001   TYR D  41 
 PHE   0.008   0.001   PHE A  63 
 TRP   0.010   0.002   TRP A  14 
 HIS   0.004   0.001   HIS A 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 4896)
  covalent geometry    : angle       0.55479 ( 6670)
  hydrogen bonds       : bond        0.03852 (  326)
  hydrogen bonds       : angle       3.83327 (  906)
  Misc. bond           : bond        0.07095 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2395.07 seconds
wall clock time: 41 minutes 33.24 seconds (2493.24 seconds total)