Starting phenix.real_space_refine
on Fri Mar 14 00:34:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yoz_33991/03_2025/7yoz_33991.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yoz_33991/03_2025/7yoz_33991.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yoz_33991/03_2025/7yoz_33991.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yoz_33991/03_2025/7yoz_33991.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yoz_33991/03_2025/7yoz_33991.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yoz_33991/03_2025/7yoz_33991.cif"
  }
  resolution = 4.3
  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=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     242      5.49       5
     S      20      5.16       5
     C    5365      2.51       5
     N    1838      2.21       5
     O    2287      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9752
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 619
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "B"
      Number of atoms: 594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 594
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
    Chain: "C"
      Number of atoms: 625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 625
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
    Chain: "D"
      Number of atoms: 568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 568
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 1, 'TRANS': 69}
    Chain: "E"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 619
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "F"
      Number of atoms: 565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 565
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 1, 'TRANS': 69}
    Chain: "G"
      Number of atoms: 625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 625
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
    Chain: "H"
      Number of atoms: 576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 576
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 1, 'TRANS': 70}
    Chain: "I"
      Number of atoms: 2463
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 2463
          Classifications: {'DNA': 121}
          Link IDs: {'rna3p': 120}
    Chain: "J"
      Number of atoms: 2498
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 2498
          Classifications: {'DNA': 121}
          Link IDs: {'rna3p': 120}
  Time building chain proxies: 7.38, per 1000 atoms: 0.76
  Number of scatterers: 9752
  At special positions: 0
  Unit cell: (122.85, 90.3, 113.4, 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)
     S      20     16.00
     P     242     15.00
     O    2287      8.00
     N    1838      7.00
     C    5365      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=0, symmetry=0
  Time building additional restraints: 2.57
  Conformation dependent library (CDL) restraints added in 551.9 milliseconds
  

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1124

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 2 sheets defined
      79.1% alpha, 0.7% beta
      120 base pairs and 215 stacking pairs defined.
    Time for finding SS restraints: 4.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 64 through 79
      removed outlier: 3.614A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.575A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.537A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.512A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 79
    Processing helix  chain 'C' and resid 85 through 114
    Processing helix  chain 'C' and resid 120 through 131
      removed outlier: 3.526A  pdb=" N   ILE C 124 " --> pdb=" O   MET C 120 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 25 through 29
    Processing helix  chain 'D' and resid 30 through 41
    Processing helix  chain 'D' and resid 49 through 77
    Processing helix  chain 'D' and resid 82 through 95
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.531A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.563A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.537A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 63 through 79
      removed outlier: 3.653A  pdb=" N   ASP G  77 " --> pdb=" O   GLU G  73 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   PHE G  78 " --> pdb=" O   ILE G  74 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 85 through 114
    Processing helix  chain 'G' and resid 120 through 132
      removed outlier: 3.593A  pdb=" N   ILE G 124 " --> pdb=" O   MET G 120 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 24 through 29
    Processing helix  chain 'H' and resid 30 through 41
    Processing helix  chain 'H' and resid 49 through 76
    Processing helix  chain 'H' and resid 82 through 93
    Processing sheet with id=AA1, first strand: chain 'C' and resid 118 through 119
    Processing sheet with id=AA2, first strand: chain 'G' and resid 83 through 84
      removed outlier: 7.722A  pdb=" N   ARG G  83 " --> pdb=" O   VAL H  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2

    350 hydrogen bonds defined for protein.
    1023 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      313 hydrogen bonds
      626 hydrogen bond angles
      0 basepair planarities
      120 basepair parallelities
      215 stacking parallelities
  Total time for adding SS restraints: 3.53

  Time building geometry restraints manager: 2.91 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1961
        1.34 -     1.45: 3358
        1.45 -     1.57: 4570
        1.57 -     1.69: 482
        1.69 -     1.81: 32
  Bond restraints: 10403
  Sorted by residual:
  bond pdb=" C3'  DT I  14 "
       pdb=" O3'  DT I  14 "
    ideal  model  delta    sigma   weight residual
    1.422  1.459 -0.037 3.00e-02 1.11e+03 1.52e+00
  bond pdb=" CB  ARG G 128 "
       pdb=" CG  ARG G 128 "
    ideal  model  delta    sigma   weight residual
    1.520  1.556 -0.036 3.00e-02 1.11e+03 1.41e+00
  bond pdb=" CD  ARG A 131 "
       pdb=" NE  ARG A 131 "
    ideal  model  delta    sigma   weight residual
    1.458  1.474 -0.016 1.40e-02 5.10e+03 1.37e+00
  bond pdb=" CG  ARG B  92 "
       pdb=" CD  ARG B  92 "
    ideal  model  delta    sigma   weight residual
    1.520  1.487  0.033 3.00e-02 1.11e+03 1.20e+00
  bond pdb=" CE  LYS G  64 "
       pdb=" NZ  LYS G  64 "
    ideal  model  delta    sigma   weight residual
    1.489  1.457  0.032 3.00e-02 1.11e+03 1.15e+00
  ... (remaining 10398 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 14709
        1.58 -     3.17: 337
        3.17 -     4.75: 13
        4.75 -     6.33: 6
        6.33 -     7.92: 3
  Bond angle restraints: 15068
  Sorted by residual:
  angle pdb=" CB  LEU A 103 "
        pdb=" CG  LEU A 103 "
        pdb=" CD1 LEU A 103 "
      ideal   model   delta    sigma   weight residual
     110.70  103.05    7.65 3.00e+00 1.11e-01 6.50e+00
  angle pdb=" N   SER C  86 "
        pdb=" CA  SER C  86 "
        pdb=" C   SER C  86 "
      ideal   model   delta    sigma   weight residual
     111.07  113.75   -2.68 1.07e+00 8.73e-01 6.25e+00
  angle pdb=" CA  LEU B  62 "
        pdb=" CB  LEU B  62 "
        pdb=" CG  LEU B  62 "
      ideal   model   delta    sigma   weight residual
     116.30  124.22   -7.92 3.50e+00 8.16e-02 5.12e+00
  angle pdb=" NE  ARG B  92 "
        pdb=" CZ  ARG B  92 "
        pdb=" NH1 ARG B  92 "
      ideal   model   delta    sigma   weight residual
     121.50  119.26    2.24 1.00e+00 1.00e+00 5.00e+00
  angle pdb=" C   LEU B  90 "
        pdb=" N   LYS B  91 "
        pdb=" CA  LYS B  91 "
      ideal   model   delta    sigma   weight residual
     120.28  123.27   -2.99 1.34e+00 5.57e-01 4.97e+00
  ... (remaining 15063 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.80: 4528
       35.80 -    71.59: 1090
       71.59 -   107.39: 15
      107.39 -   143.19: 1
      143.19 -   178.98: 3
  Dihedral angle restraints: 5637
    sinusoidal: 3911
      harmonic: 1726
  Sorted by residual:
  dihedral pdb=" C4'  DT I  14 "
           pdb=" C3'  DT I  14 "
           pdb=" O3'  DT I  14 "
           pdb=" P    DT I  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   38.98 -178.98     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DC I  51 "
           pdb=" C3'  DC I  51 "
           pdb=" O3'  DC I  51 "
           pdb=" P    DA I  52 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   36.13 -176.13     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DC I -48 "
           pdb=" C3'  DC I -48 "
           pdb=" O3'  DC I -48 "
           pdb=" P    DG I -47 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   76.24  143.76     1      3.50e+01 8.16e-04 1.42e+01
  ... (remaining 5634 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1559
       0.050 -    0.101: 141
       0.101 -    0.151: 20
       0.151 -    0.201: 1
       0.201 -    0.252: 2
  Chirality restraints: 1723
  Sorted by residual:
  chirality pdb=" CG  LEU A 103 "
            pdb=" CB  LEU A 103 "
            pdb=" CD1 LEU A 103 "
            pdb=" CD2 LEU A 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.84    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CG  LEU G 103 "
            pdb=" CB  LEU G 103 "
            pdb=" CD1 LEU G 103 "
            pdb=" CD2 LEU G 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.81    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  THR G 107 "
            pdb=" N   THR G 107 "
            pdb=" C   THR G 107 "
            pdb=" CB  THR G 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.15 2.00e-01 2.50e+01 5.80e-01
  ... (remaining 1720 not shown)

  Planarity restraints: 1069
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP E  77 "    0.024 2.00e-02 2.50e+03   5.00e-02 2.50e+01
        pdb=" CG  ASP E  77 "   -0.086 2.00e-02 2.50e+03
        pdb=" OD1 ASP E  77 "    0.031 2.00e-02 2.50e+03
        pdb=" OD2 ASP E  77 "    0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS D  31 "   -0.024 5.00e-02 4.00e+02   3.62e-02 2.09e+00
        pdb=" N   PRO D  32 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO D  32 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO D  32 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  92 "    0.031 9.50e-02 1.11e+02   1.84e-02 1.96e+00
        pdb=" NE  ARG B  92 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  92 "    0.023 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  92 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  92 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1066 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1872
        2.80 -     3.32: 8558
        3.32 -     3.85: 18168
        3.85 -     4.37: 20847
        4.37 -     4.90: 29311
  Nonbonded interactions: 78756
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NH2 ARG E 131 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" OD2 ASP A 106 "
            pdb=" NH2 ARG A 131 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" NZ  LYS C 115 "
            pdb=" OP2  DT J  29 "
     model   vdw
     2.324 3.120
  nonbonded pdb=" NE  ARG G 128 "
            pdb=" OE1 GLU G 133 "
     model   vdw
     2.359 3.120
  nonbonded pdb=" NZ  LYS G  79 "
            pdb=" OE1 GLU H  74 "
     model   vdw
     2.366 3.120
  ... (remaining 78751 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'C' and resid 59 through 134)
  selection = chain 'E'
  selection = (chain 'G' and resid 59 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 25 through 94)
  selection = (chain 'D' and resid 25 through 94)
  selection = (chain 'F' and resid 25 through 94)
  selection = (chain 'H' and resid 25 through 94)
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.580
  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:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     29.340
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
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   0.037  10403  Z= 0.171
  Angle     :  0.552   7.918  15068  Z= 0.361
  Chirality :  0.032   0.252   1723
  Planarity :  0.004   0.050   1069
  Dihedral  : 27.407 178.984   4513
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  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:  0.64 (0.30), residues: 578
  helix:  0.94 (0.21), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.23 (0.43), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A 113 
 PHE   0.014   0.001   PHE G 104 
 TYR   0.012   0.001   TYR D  88 
 ARG   0.024   0.001   ARG B  92 

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 335
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.8892 (mttm) cc_final: 0.8550 (mtmm)
REVERT: A   68 GLN cc_start: 0.8865 (tt0) cc_final: 0.8408 (tp40)
REVERT: A   85 GLN cc_start: 0.8636 (tt0) cc_final: 0.8300 (tp40)
REVERT: A   93 GLN cc_start: 0.8676 (tt0) cc_final: 0.8038 (tm-30)
REVERT: A  119 ILE cc_start: 0.9037 (pt) cc_final: 0.8346 (mt)
REVERT: A  120 MET cc_start: 0.8634 (mmm) cc_final: 0.8410 (mmm)
REVERT: A  123 ASP cc_start: 0.8834 (m-30) cc_final: 0.8472 (t70)
REVERT: A  126 LEU cc_start: 0.9647 (tp) cc_final: 0.9430 (tp)
REVERT: A  128 ARG cc_start: 0.8893 (mtp180) cc_final: 0.8313 (mtp180)
REVERT: A  130 ILE cc_start: 0.9707 (mt) cc_final: 0.9487 (mm)
REVERT: B   51 TYR cc_start: 0.8033 (m-80) cc_final: 0.7735 (m-80)
REVERT: C  104 PHE cc_start: 0.9000 (m-80) cc_final: 0.8537 (m-80)
REVERT: C  121 PRO cc_start: 0.8849 (Cg_exo) cc_final: 0.8627 (Cg_endo)
REVERT: C  123 ASP cc_start: 0.8886 (m-30) cc_final: 0.8366 (m-30)
REVERT: C  124 ILE cc_start: 0.9349 (mt) cc_final: 0.9097 (tp)
REVERT: C  130 ILE cc_start: 0.8366 (tt) cc_final: 0.8042 (tt)
REVERT: D   43 VAL cc_start: 0.8313 (t) cc_final: 0.7889 (t)
REVERT: D   52 GLU cc_start: 0.9122 (tt0) cc_final: 0.8831 (pp20)
REVERT: D   55 ARG cc_start: 0.8771 (mtt180) cc_final: 0.8372 (mmm-85)
REVERT: D   59 LYS cc_start: 0.9150 (tttt) cc_final: 0.8326 (tptt)
REVERT: D   66 ILE cc_start: 0.9140 (mm) cc_final: 0.8911 (pt)
REVERT: D   71 THR cc_start: 0.8948 (m) cc_final: 0.8443 (m)
REVERT: E   60 LEU cc_start: 0.6207 (mt) cc_final: 0.5995 (mp)
REVERT: E   70 LEU cc_start: 0.8786 (tp) cc_final: 0.8246 (tt)
REVERT: E   87 SER cc_start: 0.8980 (m) cc_final: 0.8511 (p)
REVERT: E  104 PHE cc_start: 0.8998 (m-80) cc_final: 0.8464 (m-80)
REVERT: E  109 LEU cc_start: 0.9725 (tp) cc_final: 0.9503 (tp)
REVERT: E  126 LEU cc_start: 0.9139 (tp) cc_final: 0.8919 (tt)
REVERT: F   59 LYS cc_start: 0.9204 (tttt) cc_final: 0.8908 (ttpt)
REVERT: F   66 ILE cc_start: 0.9055 (mm) cc_final: 0.8817 (pt)
REVERT: G   70 LEU cc_start: 0.9140 (tp) cc_final: 0.8380 (tt)
REVERT: G   90 MET cc_start: 0.8385 (ttm) cc_final: 0.8051 (tmm)
REVERT: G   97 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7721 (mt-10)
REVERT: G  123 ASP cc_start: 0.8589 (m-30) cc_final: 0.8368 (t70)
REVERT: H   35 ARG cc_start: 0.8395 (mtp85) cc_final: 0.7964 (ttt180)
REVERT: H   43 VAL cc_start: 0.6861 (t) cc_final: 0.5771 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 335
  average time/residue: 0.3541
  time to fit residues: 145.9897
Evaluate side-chains
  222 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:   10.0000
   chunk 60 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 62 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 72 optimal weight:   10.0000
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
G  68 GLN
G 108 ASN
** H  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.088598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.074245 restraints weight = 54234.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.075851 restraints weight = 33787.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.076984 restraints weight = 23881.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.4142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  10403  Z= 0.222
  Angle     :  0.620   8.162  15068  Z= 0.363
  Chirality :  0.035   0.147   1723
  Planarity :  0.006   0.083   1069
  Dihedral  : 31.243 179.593   3286
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 15.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  4.96 %
    Favored  : 94.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.05 (0.33), residues: 578
  helix:  1.91 (0.23), residues: 468
  sheet:  None (None), residues: 0
  loop : -1.05 (0.50), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS B  75 
 PHE   0.015   0.001   PHE G 104 
 TYR   0.020   0.002   TYR D  72 
 ARG   0.008   0.001   ARG B  35 

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 257
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9330 (mttm) cc_final: 0.8778 (mtmm)
REVERT: A   68 GLN cc_start: 0.9146 (tt0) cc_final: 0.8940 (tp-100)
REVERT: A   85 GLN cc_start: 0.9083 (tt0) cc_final: 0.8712 (tp40)
REVERT: A   93 GLN cc_start: 0.9015 (tt0) cc_final: 0.8109 (tm-30)
REVERT: A   96 CYS cc_start: 0.9079 (m) cc_final: 0.8742 (m)
REVERT: A  119 ILE cc_start: 0.9083 (pt) cc_final: 0.8803 (mt)
REVERT: A  123 ASP cc_start: 0.8827 (m-30) cc_final: 0.8366 (t70)
REVERT: A  130 ILE cc_start: 0.9753 (mt) cc_final: 0.9504 (mm)
REVERT: B   24 ASP cc_start: 0.8202 (t0) cc_final: 0.7495 (p0)
REVERT: C   90 MET cc_start: 0.9195 (ppp) cc_final: 0.8746 (ppp)
REVERT: C   93 GLN cc_start: 0.9045 (tm-30) cc_final: 0.8800 (tm-30)
REVERT: C   94 GLU cc_start: 0.9234 (pt0) cc_final: 0.8885 (pt0)
REVERT: C  100 LEU cc_start: 0.9453 (tp) cc_final: 0.9113 (tp)
REVERT: C  104 PHE cc_start: 0.9052 (m-80) cc_final: 0.8514 (m-80)
REVERT: C  106 ASP cc_start: 0.9110 (m-30) cc_final: 0.8575 (m-30)
REVERT: D   49 LEU cc_start: 0.8301 (pp) cc_final: 0.8046 (pt)
REVERT: D   53 GLU cc_start: 0.8917 (pp20) cc_final: 0.8542 (tm-30)
REVERT: D   55 ARG cc_start: 0.8931 (mtt180) cc_final: 0.8422 (mmm-85)
REVERT: D   59 LYS cc_start: 0.9093 (tttt) cc_final: 0.8181 (tptp)
REVERT: D   66 ILE cc_start: 0.9029 (mm) cc_final: 0.8815 (pt)
REVERT: E   70 LEU cc_start: 0.8761 (tp) cc_final: 0.8477 (mt)
REVERT: E   87 SER cc_start: 0.8881 (m) cc_final: 0.8459 (p)
REVERT: E   93 GLN cc_start: 0.9296 (mm110) cc_final: 0.8879 (tp40)
REVERT: E  120 MET cc_start: 0.8654 (mmp) cc_final: 0.8169 (mmm)
REVERT: E  123 ASP cc_start: 0.9076 (m-30) cc_final: 0.8876 (m-30)
REVERT: E  128 ARG cc_start: 0.8951 (mmm-85) cc_final: 0.8341 (mmm-85)
REVERT: E  129 ARG cc_start: 0.8633 (tmt-80) cc_final: 0.8207 (tpm170)
REVERT: F   49 LEU cc_start: 0.9092 (tt) cc_final: 0.8318 (tt)
REVERT: F   59 LYS cc_start: 0.9145 (tttt) cc_final: 0.8556 (ttpp)
REVERT: F   63 GLU cc_start: 0.8809 (tt0) cc_final: 0.8346 (tm-30)
REVERT: G   68 GLN cc_start: 0.8978 (tm130) cc_final: 0.8439 (tm-30)
REVERT: G   90 MET cc_start: 0.8608 (ttm) cc_final: 0.8221 (tmm)
REVERT: G   96 CYS cc_start: 0.8170 (m) cc_final: 0.7810 (m)
REVERT: G  123 ASP cc_start: 0.8762 (m-30) cc_final: 0.8328 (t70)
REVERT: H   46 ILE cc_start: 0.8817 (mp) cc_final: 0.8559 (mt)
REVERT: H   74 GLU cc_start: 0.9025 (tt0) cc_final: 0.8681 (tt0)
REVERT: H   78 ARG cc_start: 0.8297 (ptp90) cc_final: 0.7766 (ttp80)
  outliers start: 4
  outliers final: 0
  residues processed: 260
  average time/residue: 0.3088
  time to fit residues: 100.6910
Evaluate side-chains
  202 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 76 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 6 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   chunk 49 optimal weight:    5.9990
   chunk 72 optimal weight:   10.0000
   chunk 70 optimal weight:   10.0000
   chunk 71 optimal weight:    8.9990
   chunk 61 optimal weight:   10.0000
   chunk 63 optimal weight:    8.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** C  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  75 HIS
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.064029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.049169 restraints weight = 60489.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.050488 restraints weight = 36473.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.051386 restraints weight = 25918.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.9031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.093  10403  Z= 0.448
  Angle     :  0.823   7.695  15068  Z= 0.480
  Chirality :  0.043   0.201   1723
  Planarity :  0.007   0.062   1069
  Dihedral  : 33.075 178.033   3286
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 21.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  5.95 %
    Favored  : 93.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.32), residues: 578
  helix:  1.04 (0.23), residues: 455
  sheet:  None (None), residues: 0
  loop : -1.20 (0.45), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.011   0.003   HIS A 113 
 PHE   0.025   0.003   PHE G 104 
 TYR   0.019   0.003   TYR B  88 
 ARG   0.018   0.002   ARG A 134 

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 286
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.9066 (mm) cc_final: 0.8493 (mt)
REVERT: A   61 LEU cc_start: 0.9188 (tt) cc_final: 0.8884 (tp)
REVERT: A   64 LYS cc_start: 0.9593 (mttm) cc_final: 0.9296 (mtmm)
REVERT: A   68 GLN cc_start: 0.9402 (tt0) cc_final: 0.9075 (tt0)
REVERT: A   76 GLN cc_start: 0.8795 (tp-100) cc_final: 0.8587 (tp40)
REVERT: A   90 MET cc_start: 0.8331 (tmm) cc_final: 0.7790 (tmm)
REVERT: A   93 GLN cc_start: 0.9300 (tt0) cc_final: 0.7930 (tm-30)
REVERT: A   94 GLU cc_start: 0.9121 (pt0) cc_final: 0.8459 (pt0)
REVERT: A   97 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7364 (mt-10)
REVERT: A  115 LYS cc_start: 0.9105 (mmmt) cc_final: 0.8681 (mmmm)
REVERT: A  130 ILE cc_start: 0.9769 (mt) cc_final: 0.9568 (mt)
REVERT: B   24 ASP cc_start: 0.8703 (t0) cc_final: 0.8386 (t0)
REVERT: B   31 LYS cc_start: 0.9424 (mttp) cc_final: 0.9214 (mtpt)
REVERT: B   52 GLU cc_start: 0.9066 (tp30) cc_final: 0.8858 (tp30)
REVERT: B   63 GLU cc_start: 0.8803 (tt0) cc_final: 0.8213 (tp30)
REVERT: B   74 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8446 (tm-30)
REVERT: B   85 ASP cc_start: 0.9462 (m-30) cc_final: 0.9203 (m-30)
REVERT: B   92 ARG cc_start: 0.8137 (ttt180) cc_final: 0.7928 (tmm-80)
REVERT: C   78 PHE cc_start: 0.8498 (t80) cc_final: 0.8104 (t80)
REVERT: C   90 MET cc_start: 0.9104 (ppp) cc_final: 0.8506 (ppp)
REVERT: C   93 GLN cc_start: 0.9185 (tm-30) cc_final: 0.8789 (tm-30)
REVERT: D   52 GLU cc_start: 0.8980 (pp20) cc_final: 0.8779 (pp20)
REVERT: D   55 ARG cc_start: 0.9244 (mtt180) cc_final: 0.8875 (mtt-85)
REVERT: D   57 VAL cc_start: 0.9583 (t) cc_final: 0.9178 (t)
REVERT: D   59 LYS cc_start: 0.9503 (tttt) cc_final: 0.8710 (tptp)
REVERT: E   70 LEU cc_start: 0.9294 (tp) cc_final: 0.9051 (tt)
REVERT: E   76 GLN cc_start: 0.8916 (tt0) cc_final: 0.8342 (tp-100)
REVERT: E   90 MET cc_start: 0.8687 (ppp) cc_final: 0.8277 (ppp)
REVERT: E   93 GLN cc_start: 0.9408 (mm110) cc_final: 0.9108 (mm110)
REVERT: E   94 GLU cc_start: 0.8840 (pt0) cc_final: 0.8279 (pt0)
REVERT: E  119 ILE cc_start: 0.8830 (pt) cc_final: 0.8373 (pt)
REVERT: E  120 MET cc_start: 0.8648 (mmp) cc_final: 0.8100 (mmm)
REVERT: E  123 ASP cc_start: 0.9073 (m-30) cc_final: 0.8839 (m-30)
REVERT: E  128 ARG cc_start: 0.8996 (mmm-85) cc_final: 0.8779 (mmm160)
REVERT: F   36 ARG cc_start: 0.9143 (mtm110) cc_final: 0.8896 (ttp80)
REVERT: F   49 LEU cc_start: 0.9310 (tt) cc_final: 0.9053 (tp)
REVERT: F   84 MET cc_start: 0.8757 (ptt) cc_final: 0.8422 (ptt)
REVERT: F   88 TYR cc_start: 0.9075 (m-80) cc_final: 0.8441 (t80)
REVERT: G   60 LEU cc_start: 0.8531 (mm) cc_final: 0.8190 (mt)
REVERT: G   65 LEU cc_start: 0.9488 (tp) cc_final: 0.9264 (tp)
REVERT: G   73 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8719 (tm-30)
REVERT: G   76 GLN cc_start: 0.9244 (tp40) cc_final: 0.8992 (tp-100)
REVERT: G   90 MET cc_start: 0.9024 (ttm) cc_final: 0.8564 (tmm)
REVERT: G   93 GLN cc_start: 0.9188 (pt0) cc_final: 0.8174 (tm-30)
REVERT: G  128 ARG cc_start: 0.9131 (mtp-110) cc_final: 0.8180 (mtp-110)
REVERT: H   35 ARG cc_start: 0.8439 (mmt180) cc_final: 0.8106 (mmt180)
REVERT: H   39 ARG cc_start: 0.8891 (mmt90) cc_final: 0.8587 (mmt90)
REVERT: H   78 ARG cc_start: 0.8834 (ptp90) cc_final: 0.8422 (ptp90)
REVERT: H   85 ASP cc_start: 0.9215 (m-30) cc_final: 0.8996 (m-30)
REVERT: H   88 TYR cc_start: 0.8813 (m-10) cc_final: 0.8383 (m-10)
  outliers start: 3
  outliers final: 2
  residues processed: 286
  average time/residue: 0.2919
  time to fit residues: 105.7799
Evaluate side-chains
  237 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 235
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 56 optimal weight:   20.0000
   chunk 73 optimal weight:   10.0000
   chunk 51 optimal weight:    7.9990
   chunk 7 optimal weight:    8.9990
   chunk 26 optimal weight:    0.0870
   chunk 71 optimal weight:    7.9990
   chunk 25 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0980
   chunk 33 optimal weight:    9.9990
   overall best weight:    2.0162

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
E  93 GLN
G  93 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.066563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.051790 restraints weight = 59456.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.053137 restraints weight = 35334.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.054059 restraints weight = 25018.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.9230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10403  Z= 0.231
  Angle     :  0.660   7.204  15068  Z= 0.388
  Chirality :  0.035   0.152   1723
  Planarity :  0.004   0.051   1069
  Dihedral  : 32.570 178.400   3286
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 14.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  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:  1.34 (0.33), residues: 578
  helix:  1.36 (0.23), residues: 461
  sheet:  None (None), residues: 0
  loop : -0.85 (0.47), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 113 
 PHE   0.015   0.001   PHE A 104 
 TYR   0.008   0.001   TYR G  99 
 ARG   0.010   0.001   ARG A  72 

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 294
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9566 (mttm) cc_final: 0.9289 (mtmm)
REVERT: A   65 LEU cc_start: 0.9588 (tp) cc_final: 0.9339 (tp)
REVERT: A   76 GLN cc_start: 0.8730 (tp-100) cc_final: 0.8437 (tm-30)
REVERT: A   85 GLN cc_start: 0.9132 (tt0) cc_final: 0.8696 (tp40)
REVERT: A   90 MET cc_start: 0.8234 (tmm) cc_final: 0.7890 (tmm)
REVERT: A   93 GLN cc_start: 0.9018 (tt0) cc_final: 0.8607 (tt0)
REVERT: A  106 ASP cc_start: 0.9077 (t70) cc_final: 0.8845 (t70)
REVERT: A  109 LEU cc_start: 0.9437 (mt) cc_final: 0.8975 (mt)
REVERT: A  115 LYS cc_start: 0.8963 (mmmt) cc_final: 0.8741 (mmmm)
REVERT: A  120 MET cc_start: 0.9055 (mmm) cc_final: 0.8496 (mmm)
REVERT: A  128 ARG cc_start: 0.8568 (tmt-80) cc_final: 0.8283 (tpt90)
REVERT: A  131 ARG cc_start: 0.9385 (ttm170) cc_final: 0.9178 (ttm-80)
REVERT: B   24 ASP cc_start: 0.8501 (t0) cc_final: 0.7866 (p0)
REVERT: B   29 ILE cc_start: 0.9426 (pt) cc_final: 0.9176 (mt)
REVERT: B   63 GLU cc_start: 0.8621 (tt0) cc_final: 0.8030 (tp30)
REVERT: B   74 GLU cc_start: 0.8439 (tm-30) cc_final: 0.7894 (tm-30)
REVERT: B   85 ASP cc_start: 0.9405 (m-30) cc_final: 0.9171 (m-30)
REVERT: C   64 LYS cc_start: 0.9065 (mmmm) cc_final: 0.8676 (mmmm)
REVERT: C   90 MET cc_start: 0.8981 (ppp) cc_final: 0.8257 (ppp)
REVERT: C   93 GLN cc_start: 0.8029 (tm-30) cc_final: 0.6124 (tm-30)
REVERT: C   94 GLU cc_start: 0.9290 (pt0) cc_final: 0.8687 (pt0)
REVERT: C   97 GLU cc_start: 0.8273 (pt0) cc_final: 0.7797 (pt0)
REVERT: C  100 LEU cc_start: 0.9733 (tp) cc_final: 0.9468 (tt)
REVERT: C  105 GLU cc_start: 0.8883 (pt0) cc_final: 0.8602 (pp20)
REVERT: C  106 ASP cc_start: 0.8812 (m-30) cc_final: 0.8389 (m-30)
REVERT: C  129 ARG cc_start: 0.9133 (ptm-80) cc_final: 0.8909 (ttm-80)
REVERT: C  131 ARG cc_start: 0.8781 (tpp80) cc_final: 0.8313 (tpp80)
REVERT: D   53 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8757 (tm-30)
REVERT: D   55 ARG cc_start: 0.9213 (mtt180) cc_final: 0.8444 (mmm-85)
REVERT: D   63 GLU cc_start: 0.9253 (tt0) cc_final: 0.8835 (tm-30)
REVERT: D   66 ILE cc_start: 0.9494 (mt) cc_final: 0.9273 (pt)
REVERT: D   72 TYR cc_start: 0.8090 (t80) cc_final: 0.7868 (t80)
REVERT: E   68 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8379 (tp-100)
REVERT: E   76 GLN cc_start: 0.8996 (tt0) cc_final: 0.8467 (tp-100)
REVERT: E   93 GLN cc_start: 0.9357 (mm-40) cc_final: 0.9143 (mm110)
REVERT: E  119 ILE cc_start: 0.8849 (pt) cc_final: 0.8410 (pt)
REVERT: E  120 MET cc_start: 0.8619 (mmp) cc_final: 0.7938 (mmm)
REVERT: E  128 ARG cc_start: 0.8920 (mmm-85) cc_final: 0.8705 (mmm-85)
REVERT: F   50 ILE cc_start: 0.9536 (tp) cc_final: 0.8800 (tp)
REVERT: F   64 ASN cc_start: 0.9214 (t0) cc_final: 0.8850 (m-40)
REVERT: F   84 MET cc_start: 0.8678 (ptt) cc_final: 0.8465 (ptt)
REVERT: F   88 TYR cc_start: 0.8962 (m-80) cc_final: 0.8651 (t80)
REVERT: F   90 LEU cc_start: 0.8964 (tt) cc_final: 0.8628 (pp)
REVERT: G   60 LEU cc_start: 0.8251 (mm) cc_final: 0.7708 (mt)
REVERT: G   61 LEU cc_start: 0.8941 (tt) cc_final: 0.8626 (tt)
REVERT: G   90 MET cc_start: 0.8825 (ttm) cc_final: 0.8406 (tmm)
REVERT: G   93 GLN cc_start: 0.8732 (pt0) cc_final: 0.7516 (tm-30)
REVERT: G   94 GLU cc_start: 0.8655 (pt0) cc_final: 0.8257 (pt0)
REVERT: G   97 GLU cc_start: 0.8251 (mt-10) cc_final: 0.5906 (mt-10)
REVERT: G  120 MET cc_start: 0.9354 (mmp) cc_final: 0.9117 (mmm)
REVERT: G  123 ASP cc_start: 0.8645 (t70) cc_final: 0.8178 (t70)
REVERT: H   35 ARG cc_start: 0.8362 (mmt180) cc_final: 0.8080 (mmt180)
REVERT: H   39 ARG cc_start: 0.8905 (mmt90) cc_final: 0.8645 (mmt90)
REVERT: H   74 GLU cc_start: 0.9086 (tt0) cc_final: 0.8658 (tt0)
REVERT: H   78 ARG cc_start: 0.8866 (ptp90) cc_final: 0.8639 (ptp90)
REVERT: H   88 TYR cc_start: 0.8600 (m-10) cc_final: 0.8060 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 294
  average time/residue: 0.3060
  time to fit residues: 113.0868
Evaluate side-chains
  246 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 246
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 77 optimal weight:   10.0000
   chunk 11 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 23 optimal weight:    5.9990
   chunk 60 optimal weight:   10.0000
   chunk 56 optimal weight:   20.0000
   chunk 78 optimal weight:   10.0000
   chunk 76 optimal weight:    7.9990
   chunk 36 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  68 GLN
** H  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.060667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.046135 restraints weight = 59887.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.047381 restraints weight = 36421.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.048218 restraints weight = 26180.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          1.0498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  10403  Z= 0.340
  Angle     :  0.724  10.817  15068  Z= 0.423
  Chirality :  0.038   0.159   1723
  Planarity :  0.005   0.044   1069
  Dihedral  : 32.861 179.680   3286
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 20.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.32), residues: 578
  helix:  0.99 (0.23), residues: 454
  sheet:  None (None), residues: 0
  loop : -1.25 (0.43), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS A 113 
 PHE   0.019   0.002   PHE A 104 
 TYR   0.011   0.002   TYR G  99 
 ARG   0.011   0.001   ARG B  35 

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 271
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9567 (mttm) cc_final: 0.9293 (mtmt)
REVERT: A   65 LEU cc_start: 0.9637 (tp) cc_final: 0.9385 (tp)
REVERT: A   90 MET cc_start: 0.8491 (tmm) cc_final: 0.8138 (tmm)
REVERT: A   92 LEU cc_start: 0.9658 (tt) cc_final: 0.9394 (tt)
REVERT: A  105 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8201 (tm-30)
REVERT: A  106 ASP cc_start: 0.8977 (t70) cc_final: 0.8704 (t70)
REVERT: A  115 LYS cc_start: 0.9058 (mmmt) cc_final: 0.8709 (mmmm)
REVERT: A  120 MET cc_start: 0.9165 (mmm) cc_final: 0.8964 (mmm)
REVERT: A  128 ARG cc_start: 0.8568 (tmt-80) cc_final: 0.8351 (tpt-90)
REVERT: B   24 ASP cc_start: 0.8716 (t0) cc_final: 0.7664 (t0)
REVERT: B   31 LYS cc_start: 0.9494 (mttp) cc_final: 0.9178 (mtpp)
REVERT: B   63 GLU cc_start: 0.8769 (tt0) cc_final: 0.8312 (tp30)
REVERT: B   74 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8139 (tm-30)
REVERT: B   85 ASP cc_start: 0.9332 (m-30) cc_final: 0.9122 (m-30)
REVERT: C   90 MET cc_start: 0.8936 (ppp) cc_final: 0.8408 (ppp)
REVERT: C   94 GLU cc_start: 0.9280 (pt0) cc_final: 0.8962 (pt0)
REVERT: C  105 GLU cc_start: 0.8877 (pt0) cc_final: 0.8427 (pp20)
REVERT: C  106 ASP cc_start: 0.8966 (m-30) cc_final: 0.8490 (m-30)
REVERT: D   55 ARG cc_start: 0.9172 (mtt180) cc_final: 0.8783 (mtp180)
REVERT: D   63 GLU cc_start: 0.9215 (tt0) cc_final: 0.8874 (tm-30)
REVERT: E   70 LEU cc_start: 0.9531 (tt) cc_final: 0.9285 (tp)
REVERT: E   76 GLN cc_start: 0.9004 (tt0) cc_final: 0.8471 (tp-100)
REVERT: E   93 GLN cc_start: 0.9400 (mm-40) cc_final: 0.9172 (mm110)
REVERT: E  110 CYS cc_start: 0.8843 (t) cc_final: 0.8265 (t)
REVERT: E  119 ILE cc_start: 0.8807 (pt) cc_final: 0.8333 (pt)
REVERT: E  123 ASP cc_start: 0.9207 (m-30) cc_final: 0.8851 (m-30)
REVERT: F   24 ASP cc_start: 0.7828 (t0) cc_final: 0.6839 (t0)
REVERT: F   27 GLN cc_start: 0.8903 (mm-40) cc_final: 0.8665 (mm110)
REVERT: F   29 ILE cc_start: 0.9688 (mm) cc_final: 0.9232 (mm)
REVERT: F   60 VAL cc_start: 0.9028 (p) cc_final: 0.8476 (p)
REVERT: F   84 MET cc_start: 0.8813 (ptt) cc_final: 0.8532 (ptt)
REVERT: F   88 TYR cc_start: 0.8916 (m-80) cc_final: 0.8496 (t80)
REVERT: G   73 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8816 (tm-30)
REVERT: G   90 MET cc_start: 0.8758 (ttm) cc_final: 0.8375 (tmm)
REVERT: G  116 ARG cc_start: 0.9276 (mtm-85) cc_final: 0.8996 (mtm180)
REVERT: G  123 ASP cc_start: 0.8639 (t70) cc_final: 0.8331 (t70)
REVERT: G  128 ARG cc_start: 0.8861 (mtp-110) cc_final: 0.7778 (mtp-110)
REVERT: H   39 ARG cc_start: 0.8836 (mmt90) cc_final: 0.8619 (mmt90)
REVERT: H   63 GLU cc_start: 0.8633 (tt0) cc_final: 0.8362 (tt0)
REVERT: H   74 GLU cc_start: 0.9093 (tt0) cc_final: 0.8851 (tt0)
REVERT: H   78 ARG cc_start: 0.8953 (ptp90) cc_final: 0.8684 (ptp90)
REVERT: H   85 ASP cc_start: 0.9165 (m-30) cc_final: 0.8949 (m-30)
REVERT: H   88 TYR cc_start: 0.8763 (m-10) cc_final: 0.8252 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 271
  average time/residue: 0.2656
  time to fit residues: 92.9287
Evaluate side-chains
  225 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 68 optimal weight:   20.0000
   chunk 59 optimal weight:    9.9990
   chunk 79 optimal weight:   10.0000
   chunk 48 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 39 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 57 optimal weight:   10.0000
   chunk 55 optimal weight:    0.5980
   chunk 20 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A  93 GLN
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  75 HIS
** H  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.063177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.048609 restraints weight = 60024.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.049969 restraints weight = 34734.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.050858 restraints weight = 24272.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          1.0716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10403  Z= 0.226
  Angle     :  0.687  13.264  15068  Z= 0.396
  Chirality :  0.036   0.190   1723
  Planarity :  0.004   0.039   1069
  Dihedral  : 32.638 179.074   3286
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  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:  0.93 (0.32), residues: 578
  helix:  1.15 (0.23), residues: 449
  sheet:  None (None), residues: 0
  loop : -1.13 (0.46), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS D  75 
 PHE   0.017   0.002   PHE A 104 
 TYR   0.013   0.001   TYR D  72 
 ARG   0.007   0.001   ARG H  92 

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 281
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9607 (mttm) cc_final: 0.9112 (mtmm)
REVERT: A   65 LEU cc_start: 0.9628 (tp) cc_final: 0.9330 (tp)
REVERT: A   83 ARG cc_start: 0.8338 (mtp-110) cc_final: 0.8123 (mtp-110)
REVERT: A   90 MET cc_start: 0.8360 (tmm) cc_final: 0.7985 (tmm)
REVERT: B   24 ASP cc_start: 0.8266 (t0) cc_final: 0.7930 (p0)
REVERT: B   63 GLU cc_start: 0.8704 (tt0) cc_final: 0.8266 (tp30)
REVERT: B   74 GLU cc_start: 0.8554 (tm-30) cc_final: 0.7836 (tm-30)
REVERT: C   90 MET cc_start: 0.8926 (ppp) cc_final: 0.8438 (ppp)
REVERT: C  105 GLU cc_start: 0.8853 (pt0) cc_final: 0.8348 (pp20)
REVERT: C  106 ASP cc_start: 0.8996 (m-30) cc_final: 0.8521 (m-30)
REVERT: D   52 GLU cc_start: 0.8927 (pp20) cc_final: 0.8722 (pp20)
REVERT: D   55 ARG cc_start: 0.8988 (mtt180) cc_final: 0.8459 (mtp85)
REVERT: D   64 ASN cc_start: 0.9143 (t0) cc_final: 0.8905 (m-40)
REVERT: E   70 LEU cc_start: 0.9487 (tt) cc_final: 0.9242 (tp)
REVERT: E   76 GLN cc_start: 0.9003 (tt0) cc_final: 0.8448 (tp-100)
REVERT: E  110 CYS cc_start: 0.8613 (t) cc_final: 0.8254 (t)
REVERT: E  123 ASP cc_start: 0.9182 (m-30) cc_final: 0.8783 (m-30)
REVERT: F   29 ILE cc_start: 0.9585 (mm) cc_final: 0.9302 (mm)
REVERT: F   31 LYS cc_start: 0.8393 (tptp) cc_final: 0.7682 (tptp)
REVERT: F   60 VAL cc_start: 0.8882 (p) cc_final: 0.8299 (p)
REVERT: F   78 ARG cc_start: 0.7340 (ptm160) cc_final: 0.7078 (ptm160)
REVERT: F   84 MET cc_start: 0.8777 (ptt) cc_final: 0.8508 (ptt)
REVERT: F   88 TYR cc_start: 0.8811 (m-80) cc_final: 0.8469 (t80)
REVERT: F   90 LEU cc_start: 0.8895 (tt) cc_final: 0.8665 (pp)
REVERT: G   65 LEU cc_start: 0.9513 (tp) cc_final: 0.9312 (tp)
REVERT: G   83 ARG cc_start: 0.8229 (mtp-110) cc_final: 0.7839 (mmm-85)
REVERT: G   90 MET cc_start: 0.8701 (ttm) cc_final: 0.8246 (tmm)
REVERT: G  116 ARG cc_start: 0.9242 (mtm-85) cc_final: 0.8344 (mtm180)
REVERT: G  119 ILE cc_start: 0.9628 (mt) cc_final: 0.9226 (mt)
REVERT: G  120 MET cc_start: 0.9177 (mmp) cc_final: 0.7922 (mmp)
REVERT: G  123 ASP cc_start: 0.8552 (t70) cc_final: 0.8277 (t70)
REVERT: G  128 ARG cc_start: 0.8822 (mtp-110) cc_final: 0.8175 (mtp180)
REVERT: H   25 ASN cc_start: 0.9198 (p0) cc_final: 0.8938 (p0)
REVERT: H   74 GLU cc_start: 0.8982 (tt0) cc_final: 0.8515 (tt0)
REVERT: H   78 ARG cc_start: 0.8971 (ptp90) cc_final: 0.8339 (ttp80)
REVERT: H   88 TYR cc_start: 0.8537 (m-10) cc_final: 0.7872 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 281
  average time/residue: 0.2820
  time to fit residues: 101.4143
Evaluate side-chains
  239 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 70 optimal weight:   10.0000
   chunk 59 optimal weight:   10.0000
   chunk 8 optimal weight:    0.7980
   chunk 28 optimal weight:   20.0000
   chunk 5 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 54 optimal weight:    7.9990
   chunk 35 optimal weight:    0.3980
   chunk 67 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   overall best weight:    2.2386

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A  93 GLN
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.062447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.048553 restraints weight = 57197.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.049880 restraints weight = 33353.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.050763 restraints weight = 23134.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          1.1046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10403  Z= 0.240
  Angle     :  0.680   9.500  15068  Z= 0.394
  Chirality :  0.036   0.184   1723
  Planarity :  0.004   0.035   1069
  Dihedral  : 32.530 179.849   3286
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 16.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  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:  0.89 (0.33), residues: 578
  helix:  1.11 (0.23), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.10 (0.47), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS B  75 
 PHE   0.022   0.002   PHE G 104 
 TYR   0.021   0.002   TYR F  51 
 ARG   0.012   0.001   ARG H  92 

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 280
  time to evaluate  : 0.658 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9481 (mttm) cc_final: 0.9056 (mtmm)
REVERT: A   65 LEU cc_start: 0.9584 (tp) cc_final: 0.9327 (tp)
REVERT: A   68 GLN cc_start: 0.9535 (tt0) cc_final: 0.9126 (tp-100)
REVERT: A   90 MET cc_start: 0.8343 (tmm) cc_final: 0.7903 (tmm)
REVERT: A   93 GLN cc_start: 0.8844 (tt0) cc_final: 0.8416 (mt0)
REVERT: A   94 GLU cc_start: 0.9028 (pt0) cc_final: 0.8393 (pt0)
REVERT: A   97 GLU cc_start: 0.8669 (mt-10) cc_final: 0.7679 (mt-10)
REVERT: A  110 CYS cc_start: 0.8523 (p) cc_final: 0.6807 (p)
REVERT: A  123 ASP cc_start: 0.8739 (m-30) cc_final: 0.8155 (t70)
REVERT: B   31 LYS cc_start: 0.9419 (mttm) cc_final: 0.9198 (mtpt)
REVERT: B   63 GLU cc_start: 0.8755 (tt0) cc_final: 0.8374 (tp30)
REVERT: B   74 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8118 (tm-30)
REVERT: B   85 ASP cc_start: 0.9152 (m-30) cc_final: 0.8949 (m-30)
REVERT: C   90 MET cc_start: 0.8919 (ppp) cc_final: 0.8357 (ppp)
REVERT: C   94 GLU cc_start: 0.9246 (pt0) cc_final: 0.9039 (pt0)
REVERT: C  105 GLU cc_start: 0.8803 (pt0) cc_final: 0.8303 (pp20)
REVERT: C  106 ASP cc_start: 0.8855 (m-30) cc_final: 0.8336 (m-30)
REVERT: C  131 ARG cc_start: 0.8700 (tpp80) cc_final: 0.8056 (tpp80)
REVERT: D   55 ARG cc_start: 0.9052 (mtt180) cc_final: 0.8472 (mmm-85)
REVERT: D   67 ARG cc_start: 0.9166 (mtp-110) cc_final: 0.8917 (mtm110)
REVERT: E   61 LEU cc_start: 0.8957 (mp) cc_final: 0.8621 (mp)
REVERT: E   70 LEU cc_start: 0.9474 (tt) cc_final: 0.9258 (tp)
REVERT: E   76 GLN cc_start: 0.8968 (tt0) cc_final: 0.8379 (tp-100)
REVERT: E  110 CYS cc_start: 0.8505 (t) cc_final: 0.8242 (t)
REVERT: E  123 ASP cc_start: 0.8876 (m-30) cc_final: 0.8668 (m-30)
REVERT: F   29 ILE cc_start: 0.9724 (mm) cc_final: 0.9513 (mm)
REVERT: F   34 ILE cc_start: 0.9370 (tp) cc_final: 0.8703 (tp)
REVERT: F   60 VAL cc_start: 0.8907 (p) cc_final: 0.8354 (p)
REVERT: F   78 ARG cc_start: 0.7432 (ptm160) cc_final: 0.7038 (ptm160)
REVERT: F   84 MET cc_start: 0.8771 (ptt) cc_final: 0.8434 (ptt)
REVERT: F   88 TYR cc_start: 0.8758 (m-80) cc_final: 0.8493 (t80)
REVERT: G   90 MET cc_start: 0.8645 (ttm) cc_final: 0.8270 (tmm)
REVERT: G   92 LEU cc_start: 0.9669 (mm) cc_final: 0.9385 (mm)
REVERT: G  116 ARG cc_start: 0.9205 (mtm-85) cc_final: 0.8243 (mtm180)
REVERT: G  119 ILE cc_start: 0.9593 (mt) cc_final: 0.9237 (mt)
REVERT: G  120 MET cc_start: 0.9112 (mmp) cc_final: 0.8062 (mmp)
REVERT: G  123 ASP cc_start: 0.8484 (t70) cc_final: 0.8124 (t70)
REVERT: G  128 ARG cc_start: 0.8668 (mtp-110) cc_final: 0.8041 (mtp180)
REVERT: H   35 ARG cc_start: 0.8414 (mmt180) cc_final: 0.8079 (tpt170)
REVERT: H   39 ARG cc_start: 0.8676 (mmt90) cc_final: 0.8268 (mmt90)
REVERT: H   85 ASP cc_start: 0.9085 (m-30) cc_final: 0.8837 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 280
  average time/residue: 0.2884
  time to fit residues: 102.9364
Evaluate side-chains
  235 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 64 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 79 optimal weight:   10.0000
   chunk 16 optimal weight:    0.0010
   chunk 34 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   chunk 58 optimal weight:   10.0000
   chunk 53 optimal weight:    0.8980
   overall best weight:    2.1790

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  85 GLN
F  27 GLN
** H  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.062772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.048410 restraints weight = 57617.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.049751 restraints weight = 33916.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.050620 restraints weight = 23709.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          1.1291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10403  Z= 0.243
  Angle     :  0.698   9.450  15068  Z= 0.401
  Chirality :  0.037   0.220   1723
  Planarity :  0.005   0.043   1069
  Dihedral  : 32.513 179.333   3286
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 16.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  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:  0.87 (0.33), residues: 578
  helix:  1.09 (0.23), residues: 456
  sheet:  None (None), residues: 0
  loop : -1.23 (0.49), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS B  75 
 PHE   0.024   0.002   PHE G 104 
 TYR   0.013   0.002   TYR F  51 
 ARG   0.021   0.001   ARG F  35 

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 278
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9646 (mttm) cc_final: 0.9246 (mtmt)
REVERT: A   65 LEU cc_start: 0.9627 (tp) cc_final: 0.9319 (tp)
REVERT: A   90 MET cc_start: 0.8309 (tmm) cc_final: 0.7964 (tmm)
REVERT: A   93 GLN cc_start: 0.9094 (mt0) cc_final: 0.8770 (mt0)
REVERT: A   97 GLU cc_start: 0.8617 (mt-10) cc_final: 0.7806 (mt-10)
REVERT: B   24 ASP cc_start: 0.8301 (t0) cc_final: 0.7855 (t0)
REVERT: B   31 LYS cc_start: 0.9396 (mttm) cc_final: 0.9196 (mtpt)
REVERT: B   63 GLU cc_start: 0.8702 (tt0) cc_final: 0.8368 (tp30)
REVERT: B   74 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7916 (tm-30)
REVERT: B   85 ASP cc_start: 0.9191 (m-30) cc_final: 0.8979 (m-30)
REVERT: C   90 MET cc_start: 0.8839 (ppp) cc_final: 0.8302 (ppp)
REVERT: C   94 GLU cc_start: 0.9239 (pt0) cc_final: 0.8994 (pt0)
REVERT: C  105 GLU cc_start: 0.8838 (pt0) cc_final: 0.8328 (pp20)
REVERT: C  106 ASP cc_start: 0.8906 (m-30) cc_final: 0.8358 (m-30)
REVERT: D   55 ARG cc_start: 0.9054 (mtt180) cc_final: 0.8447 (mmm-85)
REVERT: D   63 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8563 (tm-30)
REVERT: D   67 ARG cc_start: 0.9184 (mtp-110) cc_final: 0.8693 (mtm110)
REVERT: E   64 LYS cc_start: 0.8655 (mmmt) cc_final: 0.8355 (mmmm)
REVERT: E   68 GLN cc_start: 0.9199 (tp40) cc_final: 0.8805 (tp40)
REVERT: E   76 GLN cc_start: 0.9006 (tt0) cc_final: 0.8380 (tp-100)
REVERT: E  103 LEU cc_start: 0.9141 (tt) cc_final: 0.8902 (pp)
REVERT: E  110 CYS cc_start: 0.8577 (t) cc_final: 0.8167 (t)
REVERT: E  123 ASP cc_start: 0.8983 (m-30) cc_final: 0.8594 (m-30)
REVERT: F   60 VAL cc_start: 0.8900 (p) cc_final: 0.8366 (p)
REVERT: F   78 ARG cc_start: 0.7465 (ptm160) cc_final: 0.7166 (ptm160)
REVERT: F   82 THR cc_start: 0.8163 (p) cc_final: 0.7820 (p)
REVERT: F   84 MET cc_start: 0.8790 (ptt) cc_final: 0.8481 (ptt)
REVERT: F   88 TYR cc_start: 0.8799 (m-80) cc_final: 0.8467 (t80)
REVERT: G   61 LEU cc_start: 0.8886 (tt) cc_final: 0.8431 (tt)
REVERT: G   73 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8739 (tm-30)
REVERT: G   90 MET cc_start: 0.8806 (ttm) cc_final: 0.8156 (tmm)
REVERT: G   92 LEU cc_start: 0.9682 (mm) cc_final: 0.9404 (mm)
REVERT: G   97 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7425 (mt-10)
REVERT: G  106 ASP cc_start: 0.9101 (t70) cc_final: 0.8645 (t70)
REVERT: G  116 ARG cc_start: 0.9242 (mtm-85) cc_final: 0.8309 (mtm180)
REVERT: G  119 ILE cc_start: 0.9639 (mt) cc_final: 0.9306 (mt)
REVERT: G  120 MET cc_start: 0.9148 (mmp) cc_final: 0.8111 (mmp)
REVERT: G  123 ASP cc_start: 0.8485 (t70) cc_final: 0.8058 (t70)
REVERT: G  128 ARG cc_start: 0.8706 (mtp-110) cc_final: 0.7679 (mtp-110)
REVERT: H   35 ARG cc_start: 0.8437 (mmt180) cc_final: 0.8050 (tpt170)
REVERT: H   74 GLU cc_start: 0.8988 (tt0) cc_final: 0.8623 (tt0)
REVERT: H   78 ARG cc_start: 0.8865 (ptt-90) cc_final: 0.8568 (ptt-90)
REVERT: H   85 ASP cc_start: 0.9082 (m-30) cc_final: 0.8756 (m-30)
REVERT: H   88 TYR cc_start: 0.8636 (m-10) cc_final: 0.7966 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 278
  average time/residue: 0.2855
  time to fit residues: 101.7001
Evaluate side-chains
  239 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 44 optimal weight:    8.9990
   chunk 27 optimal weight:    8.9990
   chunk 28 optimal weight:    9.9990
   chunk 48 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 14 optimal weight:   10.0000
   chunk 63 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.063478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.048776 restraints weight = 59258.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.050063 restraints weight = 36016.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.050957 restraints weight = 25623.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          1.1460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10403  Z= 0.233
  Angle     :  0.693   8.966  15068  Z= 0.397
  Chirality :  0.037   0.211   1723
  Planarity :  0.005   0.054   1069
  Dihedral  : 32.462 179.142   3286
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  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:  0.70 (0.33), residues: 578
  helix:  0.96 (0.23), residues: 458
  sheet:  None (None), residues: 0
  loop : -1.25 (0.52), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.017   0.002   PHE A 104 
 TYR   0.012   0.002   TYR F  51 
 ARG   0.015   0.001   ARG H  92 

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 272
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9631 (mttm) cc_final: 0.9266 (mtmt)
REVERT: A   65 LEU cc_start: 0.9606 (tp) cc_final: 0.9315 (tp)
REVERT: A   90 MET cc_start: 0.8276 (tmm) cc_final: 0.7811 (tmm)
REVERT: A   93 GLN cc_start: 0.9061 (mt0) cc_final: 0.8768 (mt0)
REVERT: A   94 GLU cc_start: 0.8991 (pt0) cc_final: 0.8618 (pt0)
REVERT: A   97 GLU cc_start: 0.8564 (mt-10) cc_final: 0.7741 (mt-10)
REVERT: B   24 ASP cc_start: 0.8307 (t0) cc_final: 0.7879 (t0)
REVERT: B   31 LYS cc_start: 0.9408 (mttm) cc_final: 0.9203 (mtpt)
REVERT: B   63 GLU cc_start: 0.8652 (tt0) cc_final: 0.8310 (tp30)
REVERT: C   90 MET cc_start: 0.8797 (ppp) cc_final: 0.8284 (ppp)
REVERT: C   94 GLU cc_start: 0.9236 (pt0) cc_final: 0.8999 (pt0)
REVERT: C  105 GLU cc_start: 0.8843 (pt0) cc_final: 0.8294 (pp20)
REVERT: C  106 ASP cc_start: 0.8972 (m-30) cc_final: 0.8260 (m-30)
REVERT: D   52 GLU cc_start: 0.8814 (pp20) cc_final: 0.8603 (pp20)
REVERT: D   55 ARG cc_start: 0.9041 (mtt180) cc_final: 0.8461 (mmm-85)
REVERT: D   57 VAL cc_start: 0.9438 (t) cc_final: 0.9103 (t)
REVERT: D   63 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8539 (tm-30)
REVERT: D   64 ASN cc_start: 0.9174 (t0) cc_final: 0.8897 (t0)
REVERT: D   67 ARG cc_start: 0.9217 (mtp-110) cc_final: 0.8786 (mtm110)
REVERT: D   78 ARG cc_start: 0.7474 (ptm-80) cc_final: 0.7146 (ptm-80)
REVERT: E   61 LEU cc_start: 0.9030 (mp) cc_final: 0.8823 (mp)
REVERT: E   64 LYS cc_start: 0.8645 (mmmt) cc_final: 0.8398 (mmmm)
REVERT: E   70 LEU cc_start: 0.9511 (tp) cc_final: 0.9095 (mt)
REVERT: E   76 GLN cc_start: 0.9022 (tt0) cc_final: 0.8499 (tp-100)
REVERT: F   39 ARG cc_start: 0.8797 (ttt-90) cc_final: 0.8198 (tpp-160)
REVERT: F   60 VAL cc_start: 0.8889 (p) cc_final: 0.8320 (p)
REVERT: F   78 ARG cc_start: 0.7525 (ptm160) cc_final: 0.7241 (ptm160)
REVERT: F   82 THR cc_start: 0.8084 (p) cc_final: 0.7712 (p)
REVERT: F   84 MET cc_start: 0.8788 (ptt) cc_final: 0.8465 (ptt)
REVERT: F   88 TYR cc_start: 0.8749 (m-80) cc_final: 0.8418 (t80)
REVERT: G   92 LEU cc_start: 0.9678 (mm) cc_final: 0.9263 (mm)
REVERT: G  106 ASP cc_start: 0.9069 (t70) cc_final: 0.8735 (t70)
REVERT: G  116 ARG cc_start: 0.9224 (mtm-85) cc_final: 0.8976 (mtm180)
REVERT: G  120 MET cc_start: 0.9053 (mmp) cc_final: 0.8772 (mmp)
REVERT: G  123 ASP cc_start: 0.8309 (t70) cc_final: 0.7972 (t70)
REVERT: G  128 ARG cc_start: 0.8697 (mtp-110) cc_final: 0.7735 (mtp-110)
REVERT: H   39 ARG cc_start: 0.8665 (mmt90) cc_final: 0.8372 (mmt90)
REVERT: H   74 GLU cc_start: 0.8972 (tt0) cc_final: 0.8610 (tt0)
REVERT: H   78 ARG cc_start: 0.8899 (ptt-90) cc_final: 0.8578 (ptt-90)
REVERT: H   85 ASP cc_start: 0.9013 (m-30) cc_final: 0.8683 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 272
  average time/residue: 0.2810
  time to fit residues: 98.6204
Evaluate side-chains
  226 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 69 optimal weight:   10.0000
   chunk 78 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 16 optimal weight:    8.9990
   chunk 76 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
G  93 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.061267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.046527 restraints weight = 59854.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.047790 restraints weight = 36083.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.048681 restraints weight = 25668.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          1.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  10403  Z= 0.278
  Angle     :  0.713   8.336  15068  Z= 0.410
  Chirality :  0.037   0.187   1723
  Planarity :  0.005   0.053   1069
  Dihedral  : 32.649 178.622   3286
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 18.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  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:  0.68 (0.33), residues: 578
  helix:  0.95 (0.23), residues: 458
  sheet:  None (None), residues: 0
  loop : -1.28 (0.51), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS H  75 
 PHE   0.026   0.002   PHE G 104 
 TYR   0.019   0.002   TYR B  72 
 ARG   0.014   0.001   ARG E 128 

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 265
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9658 (mttm) cc_final: 0.9232 (mtmm)
REVERT: A   65 LEU cc_start: 0.9621 (tp) cc_final: 0.9365 (tp)
REVERT: A   90 MET cc_start: 0.8280 (tmm) cc_final: 0.7830 (tmm)
REVERT: A   93 GLN cc_start: 0.9101 (mt0) cc_final: 0.8676 (mt0)
REVERT: A   94 GLU cc_start: 0.8953 (pt0) cc_final: 0.8624 (pt0)
REVERT: A   97 GLU cc_start: 0.8616 (mt-10) cc_final: 0.7822 (mt-10)
REVERT: A  115 LYS cc_start: 0.9111 (mmmt) cc_final: 0.8733 (mmmm)
REVERT: A  120 MET cc_start: 0.9215 (mmm) cc_final: 0.8846 (mmm)
REVERT: B   24 ASP cc_start: 0.8180 (t0) cc_final: 0.7563 (t0)
REVERT: B   27 GLN cc_start: 0.8687 (mm110) cc_final: 0.8450 (mp10)
REVERT: B   31 LYS cc_start: 0.9410 (mttm) cc_final: 0.9200 (mtpt)
REVERT: B   43 VAL cc_start: 0.9159 (t) cc_final: 0.8861 (t)
REVERT: B   63 GLU cc_start: 0.8732 (tt0) cc_final: 0.8438 (tp30)
REVERT: B   85 ASP cc_start: 0.9224 (m-30) cc_final: 0.8967 (m-30)
REVERT: C   90 MET cc_start: 0.8792 (ppp) cc_final: 0.8255 (ppp)
REVERT: C   94 GLU cc_start: 0.9265 (pt0) cc_final: 0.9012 (pt0)
REVERT: C  105 GLU cc_start: 0.8881 (pt0) cc_final: 0.8287 (pp20)
REVERT: C  106 ASP cc_start: 0.8936 (m-30) cc_final: 0.8269 (m-30)
REVERT: C  120 MET cc_start: 0.7048 (mpp) cc_final: 0.6794 (mpp)
REVERT: C  123 ASP cc_start: 0.9025 (m-30) cc_final: 0.8636 (m-30)
REVERT: D   31 LYS cc_start: 0.8924 (ttmm) cc_final: 0.8655 (ttmm)
REVERT: D   52 GLU cc_start: 0.8812 (pp20) cc_final: 0.8610 (pp20)
REVERT: D   55 ARG cc_start: 0.8985 (mtt180) cc_final: 0.8432 (mmm-85)
REVERT: D   57 VAL cc_start: 0.9544 (t) cc_final: 0.9186 (t)
REVERT: D   60 VAL cc_start: 0.9443 (p) cc_final: 0.8420 (p)
REVERT: D   78 ARG cc_start: 0.7672 (ptm-80) cc_final: 0.7308 (ptm-80)
REVERT: D   79 LYS cc_start: 0.7715 (tmmt) cc_final: 0.7406 (pttp)
REVERT: D   82 THR cc_start: 0.8767 (m) cc_final: 0.8524 (m)
REVERT: E   64 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8528 (mmmm)
REVERT: E   76 GLN cc_start: 0.9041 (tt0) cc_final: 0.8455 (tp-100)
REVERT: F   39 ARG cc_start: 0.8843 (ttt-90) cc_final: 0.8197 (tpp-160)
REVERT: F   44 LYS cc_start: 0.8687 (mptt) cc_final: 0.8383 (mmtt)
REVERT: F   60 VAL cc_start: 0.8911 (p) cc_final: 0.8372 (p)
REVERT: F   78 ARG cc_start: 0.7645 (ptm160) cc_final: 0.7316 (ptm160)
REVERT: F   82 THR cc_start: 0.8213 (p) cc_final: 0.7827 (p)
REVERT: F   84 MET cc_start: 0.8830 (ptt) cc_final: 0.8524 (ptt)
REVERT: F   88 TYR cc_start: 0.8752 (m-80) cc_final: 0.8404 (t80)
REVERT: G   92 LEU cc_start: 0.9645 (mm) cc_final: 0.9344 (mm)
REVERT: G  106 ASP cc_start: 0.9080 (t70) cc_final: 0.8688 (t70)
REVERT: G  116 ARG cc_start: 0.9261 (mtm-85) cc_final: 0.8852 (mtm180)
REVERT: G  120 MET cc_start: 0.8977 (mmp) cc_final: 0.8746 (mmp)
REVERT: G  123 ASP cc_start: 0.8305 (t70) cc_final: 0.7823 (t70)
REVERT: G  128 ARG cc_start: 0.8676 (mtp-110) cc_final: 0.7597 (mtp-110)
REVERT: H   35 ARG cc_start: 0.8269 (mmt180) cc_final: 0.7760 (tpt170)
REVERT: H   74 GLU cc_start: 0.9074 (tt0) cc_final: 0.8625 (tt0)
REVERT: H   85 ASP cc_start: 0.9166 (m-30) cc_final: 0.8836 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 265
  average time/residue: 0.2661
  time to fit residues: 90.8653
Evaluate side-chains
  226 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 79 optimal weight:   10.0000
   chunk 63 optimal weight:   10.0000
   chunk 34 optimal weight:    0.0980
   chunk 16 optimal weight:    9.9990
   chunk 76 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 62 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   overall best weight:    5.4188

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.056388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.041995 restraints weight = 61942.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.043190 restraints weight = 36285.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.044041 restraints weight = 25644.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          1.2787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062  10403  Z= 0.392
  Angle     :  0.800   9.107  15068  Z= 0.463
  Chirality :  0.041   0.195   1723
  Planarity :  0.007   0.080   1069
  Dihedral  : 33.245 178.415   3286
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 24.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  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:  0.36 (0.33), residues: 578
  helix:  0.68 (0.23), residues: 456
  sheet:  None (None), residues: 0
  loop : -1.15 (0.51), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS H  75 
 PHE   0.033   0.003   PHE G 104 
 TYR   0.029   0.003   TYR B  72 
 ARG   0.019   0.002   ARG F  35 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2944.06 seconds
wall clock time: 51 minutes 45.37 seconds (3105.37 seconds total)