Starting phenix.real_space_refine
on Thu Feb 13 02:00:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y5w_33627/02_2025/7y5w_33627.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y5w_33627/02_2025/7y5w_33627.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y5w_33627/02_2025/7y5w_33627.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y5w_33627/02_2025/7y5w_33627.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y5w_33627/02_2025/7y5w_33627.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y5w_33627/02_2025/7y5w_33627.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.017
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     202      5.49       5
     S      20      5.16       5
     C    4911      2.51       5
     N    1652      2.21       5
     O    2026      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8811
  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: 561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 561
          Classifications: {'peptide': 70}
          Link IDs: {'PTRANS': 1, 'TRANS': 68}
    Chain: "C"
      Number of atoms: 608
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 608
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 2, 'TRANS': 72}
    Chain: "D"
      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: "E"
      Number of atoms: 615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 615
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "F"
      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: "G"
      Number of atoms: 591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 591
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 2, 'TRANS': 70}
    Chain: "H"
      Number of atoms: 524
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 524
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 1, 'TRANS': 63}
    Chain: "I"
      Number of atoms: 2054
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 2054
          Classifications: {'DNA': 101}
          Link IDs: {'rna3p': 100}
    Chain: "J"
      Number of atoms: 2087
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 2087
          Classifications: {'DNA': 101}
          Link IDs: {'rna3p': 100}
  Time building chain proxies: 5.49, per 1000 atoms: 0.62
  Number of scatterers: 8811
  At special positions: 0
  Unit cell: (82, 114, 116, 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     202     15.00
     O    2026      8.00
     N    1652      7.00
     C    4911      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: 2.35
  Conformation dependent library (CDL) restraints added in 633.4 milliseconds
  

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1100

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 5 sheets defined
      79.1% alpha, 1.7% beta
      90 base pairs and 167 stacking pairs defined.
    Time for finding SS restraints: 4.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 79
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.505A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.653A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
      removed outlier: 3.501A  pdb=" N   ARG B  92 " --> pdb=" O   TYR B  88 " (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
    Processing helix  chain 'D' and resid 30 through 41
    Processing helix  chain 'D' and resid 47 through 76
      removed outlier: 4.209A  pdb=" N   TYR D  51 " --> pdb=" O   SER D  47 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   GLU D  52 " --> pdb=" O   GLY D  48 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 82 through 94
    Processing helix  chain 'E' and resid 63 through 79
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    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: 3.503A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.548A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 63 through 79
      removed outlier: 3.561A  pdb=" N   PHE G  67 " --> pdb=" O   ARG G  63 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 85 through 114
    Processing helix  chain 'G' and resid 120 through 132
      removed outlier: 3.803A  pdb=" N   ILE G 124 " --> pdb=" O   MET G 120 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLY G 132 " --> pdb=" O   ARG G 128 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 30 through 41
    Processing helix  chain 'H' and resid 49 through 77
    Processing helix  chain 'H' and resid 82 through 92
    Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 84
      removed outlier: 7.247A  pdb=" N   ARG C  83 " --> pdb=" O   VAL D  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119
    Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.326A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119

    349 hydrogen bonds defined for protein.
    1035 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      231 hydrogen bonds
      442 hydrogen bond angles
      0 basepair planarities
      90 basepair parallelities
      167 stacking parallelities
  Total time for adding SS restraints: 3.09

  Time building geometry restraints manager: 2.67 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: 1879
        1.34 -     1.45: 2816
        1.45 -     1.57: 4233
        1.57 -     1.69: 402
        1.69 -     1.81: 32
  Bond restraints: 9362
  Sorted by residual:
  bond pdb=" C3'  DG I  73 "
       pdb=" O3'  DG I  73 "
    ideal  model  delta    sigma   weight residual
    1.422  1.455 -0.033 3.00e-02 1.11e+03 1.19e+00
  bond pdb=" C3'  DG J  84 "
       pdb=" O3'  DG J  84 "
    ideal  model  delta    sigma   weight residual
    1.422  1.453 -0.031 3.00e-02 1.11e+03 1.05e+00
  bond pdb=" CG1 ILE G 112 "
       pdb=" CD1 ILE G 112 "
    ideal  model  delta    sigma   weight residual
    1.513  1.473  0.040 3.90e-02 6.57e+02 1.03e+00
  bond pdb=" CB  GLU G 105 "
       pdb=" CG  GLU G 105 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.35e-01
  bond pdb=" C3'  DG I  34 "
       pdb=" O3'  DG I  34 "
    ideal  model  delta    sigma   weight residual
    1.422  1.449 -0.027 3.00e-02 1.11e+03 8.07e-01
  ... (remaining 9357 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 13238
        1.80 -     3.61: 233
        3.61 -     5.41: 16
        5.41 -     7.22: 0
        7.22 -     9.02: 1
  Bond angle restraints: 13488
  Sorted by residual:
  angle pdb=" CB  MET B  84 "
        pdb=" CG  MET B  84 "
        pdb=" SD  MET B  84 "
      ideal   model   delta    sigma   weight residual
     112.70  121.72   -9.02 3.00e+00 1.11e-01 9.05e+00
  angle pdb=" C3'  DG I 121 "
        pdb=" C2'  DG I 121 "
        pdb=" C1'  DG I 121 "
      ideal   model   delta    sigma   weight residual
     101.60   98.09    3.51 1.50e+00 4.44e-01 5.48e+00
  angle pdb=" CB  GLU G 105 "
        pdb=" CG  GLU G 105 "
        pdb=" CD  GLU G 105 "
      ideal   model   delta    sigma   weight residual
     112.60  116.46   -3.86 1.70e+00 3.46e-01 5.16e+00
  angle pdb=" CB  ARG B  40 "
        pdb=" CG  ARG B  40 "
        pdb=" CD  ARG B  40 "
      ideal   model   delta    sigma   weight residual
     111.30  116.14   -4.84 2.30e+00 1.89e-01 4.42e+00
  angle pdb=" C2'  DG I 121 "
        pdb=" C1'  DG I 121 "
        pdb=" N9   DG I 121 "
      ideal   model   delta    sigma   weight residual
     113.50  116.46   -2.96 1.50e+00 4.44e-01 3.90e+00
  ... (remaining 13483 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.06: 3940
       29.06 -    58.13: 1086
       58.13 -    87.19: 104
       87.19 -   116.25: 1
      116.25 -   145.31: 4
  Dihedral angle restraints: 5135
    sinusoidal: 3448
      harmonic: 1687
  Sorted by residual:
  dihedral pdb=" C4'  DG I  73 "
           pdb=" C3'  DG I  73 "
           pdb=" O3'  DG I  73 "
           pdb=" P    DC I  74 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   74.69  145.31     1      3.50e+01 8.16e-04 1.43e+01
  dihedral pdb=" C4'  DT J 105 "
           pdb=" C3'  DT J 105 "
           pdb=" O3'  DT J 105 "
           pdb=" P    DG J 106 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   89.58  130.42     1      3.50e+01 8.16e-04 1.29e+01
  dihedral pdb=" C4'  DG I  34 "
           pdb=" C3'  DG I  34 "
           pdb=" O3'  DG I  34 "
           pdb=" P    DT I  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   91.20  128.80     1      3.50e+01 8.16e-04 1.27e+01
  ... (remaining 5132 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1110
       0.029 -    0.059: 327
       0.059 -    0.088: 77
       0.088 -    0.118: 29
       0.118 -    0.147: 6
  Chirality restraints: 1549
  Sorted by residual:
  chirality pdb=" CA  ILE D  29 "
            pdb=" N   ILE D  29 "
            pdb=" C   ILE D  29 "
            pdb=" CB  ILE D  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.40e-01
  chirality pdb=" CA  ILE D  46 "
            pdb=" N   ILE D  46 "
            pdb=" C   ILE D  46 "
            pdb=" CB  ILE D  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.30e-01
  chirality pdb=" CA  ILE B  29 "
            pdb=" N   ILE B  29 "
            pdb=" C   ILE B  29 "
            pdb=" CB  ILE B  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.21e-01
  ... (remaining 1546 not shown)

  Planarity restraints: 1004
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET G 120 "   -0.030 5.00e-02 4.00e+02   4.51e-02 3.26e+00
        pdb=" N   PRO G 121 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO G 121 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO G 121 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I 121 "   -0.023 2.00e-02 2.50e+03   1.04e-02 3.24e+00
        pdb=" N9   DG I 121 "    0.025 2.00e-02 2.50e+03
        pdb=" C8   DG I 121 "    0.002 2.00e-02 2.50e+03
        pdb=" N7   DG I 121 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DG I 121 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I 121 "   -0.001 2.00e-02 2.50e+03
        pdb=" O6   DG I 121 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1   DG I 121 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I 121 "   -0.004 2.00e-02 2.50e+03
        pdb=" N2   DG I 121 "    0.005 2.00e-02 2.50e+03
        pdb=" N3   DG I 121 "    0.003 2.00e-02 2.50e+03
        pdb=" C4   DG I 121 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I 110 "   -0.020 2.00e-02 2.50e+03   9.51e-03 2.04e+00
        pdb=" N1   DC I 110 "    0.016 2.00e-02 2.50e+03
        pdb=" C2   DC I 110 "    0.001 2.00e-02 2.50e+03
        pdb=" O2   DC I 110 "    0.007 2.00e-02 2.50e+03
        pdb=" N3   DC I 110 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4   DC I 110 "   -0.003 2.00e-02 2.50e+03
        pdb=" N4   DC I 110 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5   DC I 110 "    0.007 2.00e-02 2.50e+03
        pdb=" C6   DC I 110 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1001 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 219
        2.66 -     3.22: 7704
        3.22 -     3.78: 17065
        3.78 -     4.34: 20536
        4.34 -     4.90: 29648
  Nonbonded interactions: 75172
  Sorted by model distance:
  nonbonded pdb=" N2   DG I  34 "
            pdb=" O2   DC J 114 "
     model   vdw
     2.102 2.496
  nonbonded pdb=" N2   DG I  33 "
            pdb=" O2   DC J 115 "
     model   vdw
     2.118 2.496
  nonbonded pdb=" N2   DG I  85 "
            pdb=" O2   DC J  63 "
     model   vdw
     2.139 2.496
  nonbonded pdb=" O2   DC I  82 "
            pdb=" N2   DG J  66 "
     model   vdw
     2.156 2.496
  nonbonded pdb=" OG1 THR F  73 "
            pdb=" OD2 ASP F  85 "
     model   vdw
     2.228 3.040
  ... (remaining 75167 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' and resid 61 through 133)
  selection = (chain 'C' and resid 61 through 133)
  selection = (chain 'E' and resid 61 through 133)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'B' and resid 29 through 93)
  selection = (chain 'D' and resid 29 through 93)
  selection = (chain 'F' and resid 29 through 93)
  selection = chain 'H'
}

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:             0.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     25.690
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.040
  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:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6989
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   0.040   9362  Z= 0.185
  Angle     :  0.533   9.023  13488  Z= 0.314
  Chirality :  0.032   0.147   1549
  Planarity :  0.003   0.045   1004
  Dihedral  : 27.557 145.314   4035
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  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:  2.53 (0.34), residues: 563
  helix:  2.20 (0.23), residues: 458
  sheet:  None (None), residues: 0
  loop : -0.72 (0.50), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 113 
 PHE   0.007   0.001   PHE E  67 
 TYR   0.008   0.001   TYR B  51 
 ARG   0.006   0.000   ARG A 129 

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 322
  time to evaluate  : 0.736 
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: C   77 ASP cc_start: 0.6596 (t70) cc_final: 0.6280 (t0)
REVERT: E   60 LEU cc_start: 0.7308 (mt) cc_final: 0.6991 (mt)
REVERT: F   80 THR cc_start: 0.8225 (m) cc_final: 0.7965 (p)
REVERT: G   89 VAL cc_start: 0.8828 (m) cc_final: 0.8532 (m)
REVERT: G   90 MET cc_start: 0.7212 (tmm) cc_final: 0.6304 (tmm)
REVERT: H   60 VAL cc_start: 0.8165 (t) cc_final: 0.7948 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 322
  average time/residue: 0.3073
  time to fit residues: 122.1782
Evaluate side-chains
  224 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 56 optimal weight:    5.9990
   chunk 31 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    0.3980
   chunk 43 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN
C  68 GLN
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  75 HIS
E  76 GLN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.059083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.042701 restraints weight = 54682.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.043988 restraints weight = 26616.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.044817 restraints weight = 17769.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.2904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9362  Z= 0.240
  Angle     :  0.667  11.543  13488  Z= 0.373
  Chirality :  0.037   0.234   1549
  Planarity :  0.005   0.046   1004
  Dihedral  : 30.658 146.560   2840
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 17.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 26.72 %
    Favored  : 69.64 %
  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:  2.17 (0.34), residues: 563
  helix:  1.91 (0.24), residues: 463
  sheet:  None (None), residues: 0
  loop : -0.74 (0.51), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 113 
 PHE   0.022   0.002   PHE H  61 
 TYR   0.017   0.002   TYR H  88 
 ARG   0.008   0.001   ARG E  83 

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 261
  time to evaluate  : 0.713 
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: A   68 GLN cc_start: 0.9688 (mt0) cc_final: 0.9249 (mm-40)
REVERT: A   90 MET cc_start: 0.8702 (tmm) cc_final: 0.8427 (tmm)
REVERT: A   99 TYR cc_start: 0.9375 (t80) cc_final: 0.9093 (t80)
REVERT: A  112 ILE cc_start: 0.9714 (tp) cc_final: 0.9399 (pt)
REVERT: A  120 MET cc_start: 0.8620 (mtm) cc_final: 0.8144 (mtm)
REVERT: A  134 ARG cc_start: 0.8783 (tpp-160) cc_final: 0.8538 (tpp-160)
REVERT: B   44 LYS cc_start: 0.9087 (mmmt) cc_final: 0.8666 (mmmm)
REVERT: B   63 GLU cc_start: 0.9324 (mt-10) cc_final: 0.9001 (mm-30)
REVERT: B   68 ASP cc_start: 0.8581 (t70) cc_final: 0.8244 (t0)
REVERT: B   92 ARG cc_start: 0.8564 (ttp80) cc_final: 0.8302 (ttp80)
REVERT: C   73 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8660 (tm-30)
REVERT: C   77 ASP cc_start: 0.8999 (t70) cc_final: 0.8750 (t0)
REVERT: C   94 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8471 (tm-30)
REVERT: C  105 GLU cc_start: 0.9000 (tp30) cc_final: 0.8678 (mm-30)
REVERT: C  128 ARG cc_start: 0.9407 (mtp85) cc_final: 0.9091 (mtp85)
REVERT: C  129 ARG cc_start: 0.9251 (tpp80) cc_final: 0.9039 (tpp80)
REVERT: D   44 LYS cc_start: 0.9316 (ttmm) cc_final: 0.9020 (mtpp)
REVERT: E   62 ILE cc_start: 0.8809 (mt) cc_final: 0.8581 (mp)
REVERT: E  129 ARG cc_start: 0.8865 (mmm160) cc_final: 0.8337 (mmm160)
REVERT: F   31 LYS cc_start: 0.9330 (ttpp) cc_final: 0.8940 (ttmm)
REVERT: F   44 LYS cc_start: 0.9502 (OUTLIER) cc_final: 0.9206 (mmmm)
REVERT: F   79 LYS cc_start: 0.9071 (mtpp) cc_final: 0.8563 (mtmm)
REVERT: F   80 THR cc_start: 0.9367 (m) cc_final: 0.8833 (p)
REVERT: F   92 ARG cc_start: 0.8949 (tmt-80) cc_final: 0.8730 (tmt170)
REVERT: G  120 MET cc_start: 0.8588 (mmm) cc_final: 0.8369 (mmm)
REVERT: G  131 ARG cc_start: 0.8934 (mtp85) cc_final: 0.8597 (mtp85)
REVERT: H   43 VAL cc_start: 0.8291 (t) cc_final: 0.7967 (t)
REVERT: H   49 LEU cc_start: 0.8193 (mp) cc_final: 0.7890 (mm)
REVERT: H   53 GLU cc_start: 0.9420 (mt-10) cc_final: 0.9162 (mt-10)
  outliers start: 18
  outliers final: 12
  residues processed: 265
  average time/residue: 0.2802
  time to fit residues: 93.5714
Evaluate side-chains
  251 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 238
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain C residue   68 GLN
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   44 LYS
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   94 GLU
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   59 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 57 optimal weight:    7.9990
   chunk 22 optimal weight:    0.5980
   chunk 16 optimal weight:    5.9990
   chunk 11 optimal weight:    0.8980
   chunk 66 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
C  68 GLN
E  93 GLN
H  64 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.058450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.042333 restraints weight = 54920.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.043647 restraints weight = 26613.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.044463 restraints weight = 17544.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.3356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9362  Z= 0.210
  Angle     :  0.654  10.489  13488  Z= 0.368
  Chirality :  0.036   0.169   1549
  Planarity :  0.004   0.045   1004
  Dihedral  : 30.585 148.708   2840
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 16.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  6.48 %
    Allowed  : 26.92 %
    Favored  : 66.60 %
  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:  2.03 (0.34), residues: 563
  helix:  1.81 (0.24), residues: 462
  sheet:  None (None), residues: 0
  loop : -0.77 (0.51), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 113 
 PHE   0.017   0.002   PHE H  61 
 TYR   0.009   0.001   TYR F  88 
 ARG   0.006   0.001   ARG H  78 

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 259
  time to evaluate  : 0.712 
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: A   64 LYS cc_start: 0.9339 (mmmm) cc_final: 0.9119 (mmmm)
REVERT: A   74 ILE cc_start: 0.9746 (tt) cc_final: 0.9545 (tt)
REVERT: A   90 MET cc_start: 0.8719 (tmm) cc_final: 0.8188 (tmm)
REVERT: A  112 ILE cc_start: 0.9693 (tp) cc_final: 0.9393 (pt)
REVERT: A  120 MET cc_start: 0.8650 (mtm) cc_final: 0.8305 (mtm)
REVERT: A  125 GLN cc_start: 0.9316 (mt0) cc_final: 0.8983 (mm-40)
REVERT: B   44 LYS cc_start: 0.9060 (mmmt) cc_final: 0.8824 (mmmt)
REVERT: B   63 GLU cc_start: 0.9299 (mt-10) cc_final: 0.8982 (mm-30)
REVERT: B   68 ASP cc_start: 0.8624 (t70) cc_final: 0.8229 (t0)
REVERT: C   73 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8563 (tm-30)
REVERT: C   77 ASP cc_start: 0.8998 (t70) cc_final: 0.8711 (t0)
REVERT: C   85 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.9040 (mt0)
REVERT: C   94 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8391 (tm-30)
REVERT: C  125 GLN cc_start: 0.9258 (mt0) cc_final: 0.8975 (mp10)
REVERT: C  129 ARG cc_start: 0.9205 (tpp80) cc_final: 0.8876 (tpp80)
REVERT: D   44 LYS cc_start: 0.9334 (ttmm) cc_final: 0.9064 (mtpp)
REVERT: D   74 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8962 (mm-30)
REVERT: E   90 MET cc_start: 0.8970 (tpp) cc_final: 0.8752 (mmp)
REVERT: E   94 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8777 (mm-30)
REVERT: E  115 LYS cc_start: 0.9632 (mmmm) cc_final: 0.9349 (mmmm)
REVERT: E  122 LYS cc_start: 0.9585 (mtmt) cc_final: 0.9370 (ptpt)
REVERT: E  129 ARG cc_start: 0.8903 (mmm160) cc_final: 0.8301 (mmm160)
REVERT: F   31 LYS cc_start: 0.9343 (ttpp) cc_final: 0.9114 (ttmm)
REVERT: F   44 LYS cc_start: 0.9477 (OUTLIER) cc_final: 0.9224 (mmmm)
REVERT: F   79 LYS cc_start: 0.9050 (mtpp) cc_final: 0.8540 (mtmm)
REVERT: F   80 THR cc_start: 0.9407 (m) cc_final: 0.8782 (p)
REVERT: F   93 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8108 (tm-30)
REVERT: G   78 PHE cc_start: 0.8300 (t80) cc_final: 0.8096 (t80)
REVERT: G   90 MET cc_start: 0.9084 (tmm) cc_final: 0.8772 (tpp)
REVERT: G  131 ARG cc_start: 0.9027 (mtp85) cc_final: 0.8677 (mtp85)
REVERT: H   49 LEU cc_start: 0.8014 (mp) cc_final: 0.7769 (mm)
REVERT: H   53 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9159 (mt-10)
REVERT: H   67 ARG cc_start: 0.9689 (ptp-110) cc_final: 0.9478 (ptp-110)
  outliers start: 32
  outliers final: 15
  residues processed: 268
  average time/residue: 0.2933
  time to fit residues: 98.5051
Evaluate side-chains
  260 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 243
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue   85 GLN
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   44 LYS
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   46 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 74 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   chunk 27 optimal weight:    6.9990
   chunk 64 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   chunk 43 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 GLN
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** F  75 HIS ** 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 = 0.3436 r_free = 0.3436 target = 0.052777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.035953 restraints weight = 57139.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.037134 restraints weight = 28959.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.037886 restraints weight = 19622.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.4458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.055   9362  Z= 0.442
  Angle     :  0.757  11.675  13488  Z= 0.434
  Chirality :  0.042   0.195   1549
  Planarity :  0.006   0.040   1004
  Dihedral  : 31.235 154.570   2840
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 21.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  7.29 %
    Allowed  : 28.95 %
    Favored  : 63.77 %
  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:  1.77 (0.34), residues: 563
  helix:  1.60 (0.23), residues: 467
  sheet:  None (None), residues: 0
  loop : -0.80 (0.53), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS C 113 
 PHE   0.016   0.003   PHE H  61 
 TYR   0.016   0.002   TYR H  88 
 ARG   0.005   0.001   ARG F  23 

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 236
  time to evaluate  : 0.708 
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: A   64 LYS cc_start: 0.9349 (mmmm) cc_final: 0.9136 (mmmm)
REVERT: A   74 ILE cc_start: 0.9760 (tt) cc_final: 0.9541 (tt)
REVERT: A   90 MET cc_start: 0.8755 (tmm) cc_final: 0.8214 (tmm)
REVERT: A  120 MET cc_start: 0.8807 (mtm) cc_final: 0.8475 (mtm)
REVERT: A  134 ARG cc_start: 0.8784 (tpp-160) cc_final: 0.8422 (tpp-160)
REVERT: B   44 LYS cc_start: 0.9216 (mmmt) cc_final: 0.8928 (mmmt)
REVERT: B   63 GLU cc_start: 0.9331 (mt-10) cc_final: 0.9040 (mm-30)
REVERT: B   68 ASP cc_start: 0.8584 (t70) cc_final: 0.8246 (t0)
REVERT: C   73 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8604 (tm-30)
REVERT: C   77 ASP cc_start: 0.9151 (t70) cc_final: 0.8857 (t0)
REVERT: C   85 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.9087 (mt0)
REVERT: C   94 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8584 (tm-30)
REVERT: C  105 GLU cc_start: 0.9189 (tp30) cc_final: 0.8939 (mm-30)
REVERT: C  128 ARG cc_start: 0.9459 (mtp85) cc_final: 0.9205 (mtp85)
REVERT: D   44 LYS cc_start: 0.9368 (ttmm) cc_final: 0.9105 (mmmm)
REVERT: D   79 LYS cc_start: 0.8935 (mmmm) cc_final: 0.8672 (mmtt)
REVERT: E   63 ARG cc_start: 0.8812 (mmp80) cc_final: 0.8511 (mmp80)
REVERT: E   79 LYS cc_start: 0.8604 (tptt) cc_final: 0.8276 (tptp)
REVERT: E   87 SER cc_start: 0.9645 (OUTLIER) cc_final: 0.9326 (t)
REVERT: E  120 MET cc_start: 0.8596 (mmm) cc_final: 0.8125 (mmm)
REVERT: E  122 LYS cc_start: 0.9567 (mtmt) cc_final: 0.9349 (ptpt)
REVERT: E  129 ARG cc_start: 0.8937 (mmm160) cc_final: 0.8333 (mmm160)
REVERT: F   44 LYS cc_start: 0.9524 (OUTLIER) cc_final: 0.9145 (mmmm)
REVERT: F   53 GLU cc_start: 0.9483 (tp30) cc_final: 0.9196 (tp30)
REVERT: F   79 LYS cc_start: 0.9024 (mtpp) cc_final: 0.8529 (mtmm)
REVERT: F   80 THR cc_start: 0.9475 (m) cc_final: 0.9030 (p)
REVERT: F   84 MET cc_start: 0.9187 (mmp) cc_final: 0.8845 (mmm)
REVERT: F   93 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8256 (tm-30)
REVERT: G   90 MET cc_start: 0.9046 (tmm) cc_final: 0.8737 (tmm)
REVERT: G  125 GLN cc_start: 0.9703 (mm-40) cc_final: 0.9312 (mm-40)
REVERT: G  131 ARG cc_start: 0.8924 (mtp85) cc_final: 0.8575 (mtp85)
REVERT: H   43 VAL cc_start: 0.8111 (t) cc_final: 0.7807 (t)
REVERT: H   49 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8108 (mm)
REVERT: H   50 ILE cc_start: 0.8906 (pt) cc_final: 0.8555 (pt)
REVERT: H   53 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8809 (mt-10)
  outliers start: 36
  outliers final: 25
  residues processed: 250
  average time/residue: 0.2931
  time to fit residues: 91.9351
Evaluate side-chains
  246 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 217
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue   85 GLN
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  124 ILE
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  106 ASP
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   44 LYS
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue  124 ILE
Chi-restraints excluded: chain H residue   46 ILE
Chi-restraints excluded: chain H residue   49 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 74 optimal weight:    8.9990
   chunk 49 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 9 optimal weight:    0.0370
   chunk 7 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 57 optimal weight:    6.9990
   overall best weight:    1.4062

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.055259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.038483 restraints weight = 55038.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.039720 restraints weight = 27647.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.040519 restraints weight = 18648.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.4396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9362  Z= 0.241
  Angle     :  0.690  11.193  13488  Z= 0.388
  Chirality :  0.037   0.161   1549
  Planarity :  0.004   0.041   1004
  Dihedral  : 31.059 154.134   2840
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 17.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  6.48 %
    Allowed  : 31.38 %
    Favored  : 62.15 %
  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:  1.86 (0.34), residues: 563
  helix:  1.69 (0.23), residues: 466
  sheet:  None (None), residues: 0
  loop : -0.95 (0.49), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 113 
 PHE   0.014   0.002   PHE G  67 
 TYR   0.015   0.001   TYR H  88 
 ARG   0.007   0.001   ARG F  92 

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 242
  time to evaluate  : 0.673 
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   74 ILE cc_start: 0.9754 (tt) cc_final: 0.9483 (tt)
REVERT: A   90 MET cc_start: 0.8727 (tmm) cc_final: 0.8179 (tmm)
REVERT: A  112 ILE cc_start: 0.9687 (tp) cc_final: 0.9436 (pt)
REVERT: A  120 MET cc_start: 0.8684 (mtm) cc_final: 0.8338 (mtm)
REVERT: A  125 GLN cc_start: 0.9304 (mt0) cc_final: 0.8966 (mm-40)
REVERT: B   44 LYS cc_start: 0.9055 (mmmt) cc_final: 0.8638 (mmmt)
REVERT: B   63 GLU cc_start: 0.9264 (mt-10) cc_final: 0.9006 (mm-30)
REVERT: B   68 ASP cc_start: 0.8583 (t70) cc_final: 0.8268 (t0)
REVERT: C   61 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8082 (mp)
REVERT: C   63 ARG cc_start: 0.8351 (mmp-170) cc_final: 0.8028 (mmp-170)
REVERT: C   73 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8643 (tm-30)
REVERT: C   85 GLN cc_start: 0.9338 (OUTLIER) cc_final: 0.9089 (mt0)
REVERT: C   94 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8511 (tm-30)
REVERT: C  105 GLU cc_start: 0.9151 (tp30) cc_final: 0.8670 (mm-30)
REVERT: C  107 THR cc_start: 0.9677 (m) cc_final: 0.9346 (t)
REVERT: C  125 GLN cc_start: 0.9250 (mt0) cc_final: 0.8941 (mp10)
REVERT: C  128 ARG cc_start: 0.9171 (mtp85) cc_final: 0.8872 (mtp85)
REVERT: C  129 ARG cc_start: 0.9270 (tpp80) cc_final: 0.8869 (tpp80)
REVERT: D   72 TYR cc_start: 0.9120 (m-80) cc_final: 0.8914 (m-80)
REVERT: E   87 SER cc_start: 0.9567 (m) cc_final: 0.9239 (t)
REVERT: E   94 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8743 (mm-30)
REVERT: E  120 MET cc_start: 0.8628 (mmm) cc_final: 0.8089 (mmm)
REVERT: E  122 LYS cc_start: 0.9558 (mtmt) cc_final: 0.9332 (ptpt)
REVERT: F   31 LYS cc_start: 0.9381 (ttpp) cc_final: 0.9103 (ttmm)
REVERT: F   35 ARG cc_start: 0.9400 (ttp80) cc_final: 0.8870 (ttm-80)
REVERT: F   44 LYS cc_start: 0.9488 (OUTLIER) cc_final: 0.9240 (mmmm)
REVERT: F   50 ILE cc_start: 0.9342 (mm) cc_final: 0.8973 (mm)
REVERT: F   74 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8997 (mt-10)
REVERT: F   79 LYS cc_start: 0.9054 (mtpp) cc_final: 0.8517 (mtmm)
REVERT: F   80 THR cc_start: 0.9455 (m) cc_final: 0.8923 (p)
REVERT: F   84 MET cc_start: 0.9140 (mmp) cc_final: 0.8911 (mmm)
REVERT: F   93 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8130 (tm-30)
REVERT: G   90 MET cc_start: 0.9041 (tmm) cc_final: 0.8752 (tmm)
REVERT: G  131 ARG cc_start: 0.8963 (mtp85) cc_final: 0.8610 (mtp85)
REVERT: H   49 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8100 (mm)
REVERT: H   50 ILE cc_start: 0.8922 (pt) cc_final: 0.8644 (pt)
REVERT: H   53 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8931 (mt-10)
REVERT: H   63 GLU cc_start: 0.9613 (tm-30) cc_final: 0.9379 (tm-30)
REVERT: H   64 ASN cc_start: 0.9540 (p0) cc_final: 0.9307 (p0)
REVERT: H   67 ARG cc_start: 0.9698 (ptp-110) cc_final: 0.9470 (mtm110)
  outliers start: 32
  outliers final: 18
  residues processed: 253
  average time/residue: 0.2952
  time to fit residues: 93.2062
Evaluate side-chains
  256 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 234
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue   85 GLN
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  124 ILE
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   44 LYS
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   61 LEU
Chi-restraints excluded: chain G residue   69 ARG
Chi-restraints excluded: chain G residue  124 ILE
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   49 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 57 optimal weight:    7.9990
   chunk 64 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.4980
   chunk 36 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    2.0988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.054320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.037688 restraints weight = 54472.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.038917 restraints weight = 27114.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.039704 restraints weight = 18220.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.4647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9362  Z= 0.284
  Angle     :  0.715  12.936  13488  Z= 0.397
  Chirality :  0.037   0.194   1549
  Planarity :  0.004   0.044   1004
  Dihedral  : 31.042 155.957   2840
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 18.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 33.60 %
    Favored  : 60.32 %
  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:  1.86 (0.34), residues: 563
  helix:  1.74 (0.23), residues: 466
  sheet:  None (None), residues: 0
  loop : -1.20 (0.47), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 113 
 PHE   0.014   0.002   PHE G  67 
 TYR   0.017   0.002   TYR H  88 
 ARG   0.006   0.001   ARG G  69 

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 239
  time to evaluate  : 0.822 
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   74 ILE cc_start: 0.9778 (tt) cc_final: 0.9480 (tt)
REVERT: A   90 MET cc_start: 0.8742 (tmm) cc_final: 0.8187 (tmm)
REVERT: A  112 ILE cc_start: 0.9699 (tp) cc_final: 0.9436 (pt)
REVERT: A  120 MET cc_start: 0.8692 (mtm) cc_final: 0.8395 (mtm)
REVERT: B   44 LYS cc_start: 0.9235 (mmmt) cc_final: 0.8828 (mmmt)
REVERT: B   53 GLU cc_start: 0.9361 (tp30) cc_final: 0.8985 (tp30)
REVERT: B   63 GLU cc_start: 0.9276 (mt-10) cc_final: 0.9066 (mm-30)
REVERT: B   68 ASP cc_start: 0.8609 (t70) cc_final: 0.8238 (t0)
REVERT: C   61 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8362 (mp)
REVERT: C   73 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8682 (tm-30)
REVERT: C   85 GLN cc_start: 0.9325 (OUTLIER) cc_final: 0.9094 (mt0)
REVERT: C   94 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8553 (tm-30)
REVERT: C  105 GLU cc_start: 0.9138 (tp30) cc_final: 0.8760 (mm-30)
REVERT: C  107 THR cc_start: 0.9674 (m) cc_final: 0.9345 (t)
REVERT: C  125 GLN cc_start: 0.9256 (mt0) cc_final: 0.8945 (mp10)
REVERT: C  129 ARG cc_start: 0.9276 (tpp80) cc_final: 0.8859 (tpp80)
REVERT: D   79 LYS cc_start: 0.8956 (mmmm) cc_final: 0.8700 (mmtt)
REVERT: E   79 LYS cc_start: 0.8483 (tptt) cc_final: 0.8198 (tptp)
REVERT: E   87 SER cc_start: 0.9579 (OUTLIER) cc_final: 0.9260 (t)
REVERT: E  120 MET cc_start: 0.8689 (mmm) cc_final: 0.8042 (mmm)
REVERT: E  122 LYS cc_start: 0.9554 (mtmt) cc_final: 0.9341 (ptpt)
REVERT: F   31 LYS cc_start: 0.9381 (ttpp) cc_final: 0.9107 (ttmm)
REVERT: F   35 ARG cc_start: 0.9417 (ttp80) cc_final: 0.8900 (ttm-80)
REVERT: F   44 LYS cc_start: 0.9502 (OUTLIER) cc_final: 0.9148 (mmmm)
REVERT: F   79 LYS cc_start: 0.9047 (mtpp) cc_final: 0.8513 (mtmm)
REVERT: F   80 THR cc_start: 0.9469 (m) cc_final: 0.8949 (p)
REVERT: F   84 MET cc_start: 0.9148 (mmp) cc_final: 0.8935 (mmm)
REVERT: F   92 ARG cc_start: 0.9036 (tmt-80) cc_final: 0.7901 (tmt-80)
REVERT: F   93 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8191 (tm-30)
REVERT: G   78 PHE cc_start: 0.8934 (t80) cc_final: 0.7613 (t80)
REVERT: G   90 MET cc_start: 0.9020 (tmm) cc_final: 0.8700 (tmm)
REVERT: G   94 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8849 (mp0)
REVERT: G  125 GLN cc_start: 0.9720 (mm-40) cc_final: 0.9408 (mm-40)
REVERT: G  131 ARG cc_start: 0.8970 (mtp85) cc_final: 0.8623 (mtp85)
REVERT: H   29 ILE cc_start: 0.8693 (mm) cc_final: 0.8480 (tp)
REVERT: H   49 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8085 (mm)
REVERT: H   53 GLU cc_start: 0.9289 (mt-10) cc_final: 0.8891 (mt-10)
REVERT: H   63 GLU cc_start: 0.9600 (tm-30) cc_final: 0.9261 (tm-30)
  outliers start: 30
  outliers final: 20
  residues processed: 250
  average time/residue: 0.2898
  time to fit residues: 90.9206
Evaluate side-chains
  256 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 230
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue   85 GLN
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  124 ILE
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  106 ASP
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   44 LYS
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   61 LEU
Chi-restraints excluded: chain G residue   94 GLU
Chi-restraints excluded: chain G residue  124 ILE
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   49 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 7 optimal weight:    0.0070
   chunk 8 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 70 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 65 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.7398

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
F  64 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.055971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.039656 restraints weight = 54750.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.040942 restraints weight = 27363.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.041775 restraints weight = 18296.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.4747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9362  Z= 0.229
  Angle     :  0.723  15.663  13488  Z= 0.397
  Chirality :  0.036   0.158   1549
  Planarity :  0.006   0.110   1004
  Dihedral  : 30.908 156.103   2840
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 15.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 35.83 %
    Favored  : 58.70 %
  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:  1.80 (0.34), residues: 563
  helix:  1.71 (0.23), residues: 460
  sheet:  None (None), residues: 0
  loop : -1.09 (0.48), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 113 
 PHE   0.023   0.002   PHE G  78 
 TYR   0.017   0.002   TYR A  99 
 ARG   0.018   0.001   ARG H  67 

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 243
  time to evaluate  : 0.701 
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   74 ILE cc_start: 0.9773 (tt) cc_final: 0.9521 (tt)
REVERT: A   90 MET cc_start: 0.8710 (tmm) cc_final: 0.8060 (tmm)
REVERT: A  112 ILE cc_start: 0.9660 (tp) cc_final: 0.9425 (pt)
REVERT: A  120 MET cc_start: 0.8686 (mtm) cc_final: 0.8238 (mtm)
REVERT: B   44 LYS cc_start: 0.9195 (mmmt) cc_final: 0.8786 (mmmt)
REVERT: B   53 GLU cc_start: 0.9325 (tp30) cc_final: 0.8864 (tp30)
REVERT: B   63 GLU cc_start: 0.9234 (mt-10) cc_final: 0.9014 (mm-30)
REVERT: B   68 ASP cc_start: 0.8645 (t70) cc_final: 0.8264 (t0)
REVERT: C   61 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8082 (mp)
REVERT: C   63 ARG cc_start: 0.8245 (mmp-170) cc_final: 0.7938 (mmp-170)
REVERT: C   73 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8692 (tm-30)
REVERT: C   85 GLN cc_start: 0.9315 (OUTLIER) cc_final: 0.8951 (mt0)
REVERT: C   94 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8541 (tm-30)
REVERT: C  105 GLU cc_start: 0.9131 (tp30) cc_final: 0.8756 (mm-30)
REVERT: C  107 THR cc_start: 0.9657 (m) cc_final: 0.9309 (t)
REVERT: C  125 GLN cc_start: 0.9256 (mt0) cc_final: 0.8920 (mp10)
REVERT: C  129 ARG cc_start: 0.9203 (tpp80) cc_final: 0.8804 (tpt-90)
REVERT: D   79 LYS cc_start: 0.8960 (mmmm) cc_final: 0.8687 (mmtt)
REVERT: E   87 SER cc_start: 0.9515 (m) cc_final: 0.9186 (t)
REVERT: E  120 MET cc_start: 0.8625 (mmm) cc_final: 0.8078 (mmm)
REVERT: E  122 LYS cc_start: 0.9546 (mtmt) cc_final: 0.9290 (ptmt)
REVERT: F   31 LYS cc_start: 0.9403 (ttpp) cc_final: 0.9191 (ttpp)
REVERT: F   44 LYS cc_start: 0.9489 (OUTLIER) cc_final: 0.9259 (mmmt)
REVERT: F   74 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8925 (mt-10)
REVERT: F   79 LYS cc_start: 0.9063 (mtpp) cc_final: 0.8511 (mtmm)
REVERT: F   80 THR cc_start: 0.9420 (m) cc_final: 0.8811 (p)
REVERT: F   84 MET cc_start: 0.9058 (mmp) cc_final: 0.8840 (mmm)
REVERT: F   93 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8122 (tm-30)
REVERT: G   90 MET cc_start: 0.9097 (tmm) cc_final: 0.8832 (tmm)
REVERT: G   94 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8838 (mp0)
REVERT: G  123 ASP cc_start: 0.7962 (m-30) cc_final: 0.7317 (t70)
REVERT: G  131 ARG cc_start: 0.8939 (mtp85) cc_final: 0.8604 (mtp85)
REVERT: H   29 ILE cc_start: 0.8912 (mm) cc_final: 0.8045 (tp)
REVERT: H   49 LEU cc_start: 0.8335 (mp) cc_final: 0.7946 (mm)
REVERT: H   53 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8899 (mt-10)
  outliers start: 27
  outliers final: 16
  residues processed: 250
  average time/residue: 0.2898
  time to fit residues: 90.8855
Evaluate side-chains
  253 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 233
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   85 GLN
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  124 ILE
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   44 LYS
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   94 GLU
Chi-restraints excluded: chain G residue  124 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 14 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   chunk 65 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 73 optimal weight:    7.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
F  25 ASN
G  93 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.056687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.040214 restraints weight = 55071.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.041423 restraints weight = 27882.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.042212 restraints weight = 18891.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.4928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9362  Z= 0.230
  Angle     :  0.735  16.594  13488  Z= 0.401
  Chirality :  0.037   0.282   1549
  Planarity :  0.005   0.077   1004
  Dihedral  : 30.793 156.627   2840
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 17.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 34.82 %
    Favored  : 60.12 %
  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:  1.79 (0.34), residues: 563
  helix:  1.68 (0.23), residues: 460
  sheet:  None (None), residues: 0
  loop : -0.97 (0.50), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 113 
 PHE   0.025   0.002   PHE G  78 
 TYR   0.015   0.002   TYR H  88 
 ARG   0.009   0.001   ARG H  67 

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 242
  time to evaluate  : 0.746 
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: A   74 ILE cc_start: 0.9763 (tt) cc_final: 0.9402 (tt)
REVERT: A   90 MET cc_start: 0.8654 (tmm) cc_final: 0.7960 (tmm)
REVERT: A  112 ILE cc_start: 0.9672 (tp) cc_final: 0.9398 (pt)
REVERT: A  120 MET cc_start: 0.8656 (mtm) cc_final: 0.8261 (mtm)
REVERT: A  128 ARG cc_start: 0.9088 (mtp180) cc_final: 0.8593 (mtp-110)
REVERT: B   44 LYS cc_start: 0.9224 (mmmt) cc_final: 0.8819 (mmmt)
REVERT: B   53 GLU cc_start: 0.9286 (tp30) cc_final: 0.8842 (tp30)
REVERT: B   63 GLU cc_start: 0.9234 (mt-10) cc_final: 0.9031 (mm-30)
REVERT: B   68 ASP cc_start: 0.8676 (t70) cc_final: 0.8259 (t0)
REVERT: C   61 LEU cc_start: 0.8561 (mm) cc_final: 0.8286 (mp)
REVERT: C   73 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8750 (tm-30)
REVERT: C   85 GLN cc_start: 0.9289 (OUTLIER) cc_final: 0.8950 (mt0)
REVERT: C   94 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8542 (tm-30)
REVERT: C  105 GLU cc_start: 0.9123 (tp30) cc_final: 0.8736 (mm-30)
REVERT: C  107 THR cc_start: 0.9678 (m) cc_final: 0.9276 (t)
REVERT: C  125 GLN cc_start: 0.9213 (mt0) cc_final: 0.8884 (mp10)
REVERT: C  129 ARG cc_start: 0.9101 (tpp80) cc_final: 0.8731 (tpt-90)
REVERT: E   79 LYS cc_start: 0.8423 (tptt) cc_final: 0.7996 (tptp)
REVERT: E   82 LEU cc_start: 0.9335 (tp) cc_final: 0.8938 (mm)
REVERT: E   85 GLN cc_start: 0.9478 (mt0) cc_final: 0.9196 (mt0)
REVERT: E   87 SER cc_start: 0.9497 (m) cc_final: 0.9178 (t)
REVERT: E  120 MET cc_start: 0.8607 (mmm) cc_final: 0.8159 (mmm)
REVERT: F   31 LYS cc_start: 0.9388 (ttpp) cc_final: 0.9111 (ttmm)
REVERT: F   35 ARG cc_start: 0.9345 (ttp80) cc_final: 0.8926 (ttm-80)
REVERT: F   44 LYS cc_start: 0.9483 (OUTLIER) cc_final: 0.9138 (mmmm)
REVERT: F   49 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.8937 (tp)
REVERT: F   74 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8838 (mt-10)
REVERT: F   79 LYS cc_start: 0.9075 (mtpp) cc_final: 0.8563 (mtmm)
REVERT: F   80 THR cc_start: 0.9413 (m) cc_final: 0.8808 (p)
REVERT: F   84 MET cc_start: 0.9004 (mmp) cc_final: 0.8781 (mmm)
REVERT: F   88 TYR cc_start: 0.8509 (m-10) cc_final: 0.8186 (m-10)
REVERT: F   93 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8031 (tm-30)
REVERT: G   90 MET cc_start: 0.9085 (tmm) cc_final: 0.8737 (tmm)
REVERT: G   94 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8781 (mp0)
REVERT: G  123 ASP cc_start: 0.8003 (m-30) cc_final: 0.7461 (t70)
REVERT: H   49 LEU cc_start: 0.8118 (mp) cc_final: 0.7825 (mm)
REVERT: H   50 ILE cc_start: 0.8860 (pt) cc_final: 0.8506 (pt)
REVERT: H   53 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8720 (mt-10)
  outliers start: 25
  outliers final: 17
  residues processed: 247
  average time/residue: 0.2961
  time to fit residues: 91.9304
Evaluate side-chains
  251 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 230
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   85 GLN
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  124 ILE
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  106 ASP
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   44 LYS
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   94 GLU
Chi-restraints excluded: chain G residue  113 HIS
Chi-restraints excluded: chain G residue  124 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 40 optimal weight:    4.9990
   chunk 68 optimal weight:    5.9990
   chunk 54 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 42 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 70 optimal weight:    6.9990
   chunk 63 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    3.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  93 GLN
G 108 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.052943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.036399 restraints weight = 56102.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.037573 restraints weight = 27995.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.038341 restraints weight = 18832.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.5229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.046   9362  Z= 0.376
  Angle     :  0.811  17.364  13488  Z= 0.444
  Chirality :  0.041   0.294   1549
  Planarity :  0.005   0.076   1004
  Dihedral  : 31.157 157.729   2840
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 21.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 37.25 %
    Favored  : 57.89 %
  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:  1.65 (0.34), residues: 563
  helix:  1.61 (0.24), residues: 461
  sheet:  None (None), residues: 0
  loop : -1.22 (0.50), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 113 
 PHE   0.020   0.002   PHE G  67 
 TYR   0.014   0.002   TYR H  72 
 ARG   0.007   0.001   ARG F  23 

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 231
  time to evaluate  : 0.720 
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   74 ILE cc_start: 0.9747 (tt) cc_final: 0.9492 (tt)
REVERT: A   90 MET cc_start: 0.8685 (tmm) cc_final: 0.8076 (tmm)
REVERT: A  112 ILE cc_start: 0.9719 (tp) cc_final: 0.9421 (pt)
REVERT: A  120 MET cc_start: 0.8780 (mtm) cc_final: 0.8355 (mtm)
REVERT: B   44 LYS cc_start: 0.9263 (mmmt) cc_final: 0.8978 (mmmt)
REVERT: B   68 ASP cc_start: 0.8686 (t70) cc_final: 0.8277 (t0)
REVERT: C   63 ARG cc_start: 0.8394 (mmp-170) cc_final: 0.8051 (mmp-170)
REVERT: C   73 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8725 (tm-30)
REVERT: C   85 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.9067 (mt0)
REVERT: C   94 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8588 (tm-30)
REVERT: C  105 GLU cc_start: 0.9155 (tp30) cc_final: 0.8780 (mm-30)
REVERT: C  107 THR cc_start: 0.9672 (m) cc_final: 0.9354 (t)
REVERT: C  128 ARG cc_start: 0.9236 (mtp85) cc_final: 0.8911 (mtp85)
REVERT: C  129 ARG cc_start: 0.9222 (tpp80) cc_final: 0.8864 (tpp80)
REVERT: D   31 LYS cc_start: 0.9037 (ttmm) cc_final: 0.8652 (ttmm)
REVERT: D   79 LYS cc_start: 0.8927 (mmmm) cc_final: 0.8650 (mmtt)
REVERT: E   87 SER cc_start: 0.9549 (m) cc_final: 0.9248 (t)
REVERT: E  105 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8771 (mm-30)
REVERT: F   44 LYS cc_start: 0.9511 (OUTLIER) cc_final: 0.9137 (mmmm)
REVERT: F   49 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.8874 (tp)
REVERT: F   53 GLU cc_start: 0.9461 (tp30) cc_final: 0.9233 (tp30)
REVERT: F   79 LYS cc_start: 0.9029 (mtpp) cc_final: 0.8529 (mtmm)
REVERT: F   80 THR cc_start: 0.9452 (m) cc_final: 0.9051 (p)
REVERT: F   84 MET cc_start: 0.9120 (mmp) cc_final: 0.8886 (mmm)
REVERT: F   93 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8103 (tm-30)
REVERT: G   90 MET cc_start: 0.9102 (tmm) cc_final: 0.8799 (tmm)
REVERT: G   94 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8819 (mp0)
REVERT: G  123 ASP cc_start: 0.7941 (m-30) cc_final: 0.7517 (t70)
REVERT: H   53 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8620 (mt-10)
  outliers start: 24
  outliers final: 16
  residues processed: 238
  average time/residue: 0.2874
  time to fit residues: 85.8770
Evaluate side-chains
  244 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 223
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   85 GLN
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  124 ILE
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  105 GLU
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   44 LYS
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   94 GLU
Chi-restraints excluded: chain G residue  113 HIS
Chi-restraints excluded: chain G residue  124 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 44 optimal weight:    0.4980
   chunk 50 optimal weight:    8.9990
   chunk 54 optimal weight:    7.9990
   chunk 37 optimal weight:    0.3980
   chunk 55 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 125 GLN
** D  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.054863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.038310 restraints weight = 55527.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.039555 restraints weight = 27878.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.040354 restraints weight = 18734.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.5332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   9362  Z= 0.264
  Angle     :  0.826  18.007  13488  Z= 0.439
  Chirality :  0.039   0.307   1549
  Planarity :  0.005   0.071   1004
  Dihedral  : 31.078 157.000   2840
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 19.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 39.27 %
    Favored  : 56.68 %
  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:  1.62 (0.34), residues: 563
  helix:  1.56 (0.23), residues: 461
  sheet:  None (None), residues: 0
  loop : -1.07 (0.53), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 113 
 PHE   0.024   0.002   PHE G  67 
 TYR   0.012   0.001   TYR H  72 
 ARG   0.007   0.001   ARG G 128 

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 238
  time to evaluate  : 0.550 
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   74 ILE cc_start: 0.9693 (tt) cc_final: 0.9234 (tt)
REVERT: A   90 MET cc_start: 0.8627 (tmm) cc_final: 0.7896 (tmm)
REVERT: A  112 ILE cc_start: 0.9686 (tp) cc_final: 0.9415 (pt)
REVERT: A  120 MET cc_start: 0.8695 (mtm) cc_final: 0.8259 (mtm)
REVERT: A  128 ARG cc_start: 0.9159 (mtp180) cc_final: 0.8643 (mtp-110)
REVERT: B   44 LYS cc_start: 0.9240 (mmmt) cc_final: 0.8904 (mmmt)
REVERT: B   53 GLU cc_start: 0.9207 (tp30) cc_final: 0.8792 (tp30)
REVERT: B   59 LYS cc_start: 0.9274 (ttmm) cc_final: 0.8937 (ttmm)
REVERT: B   63 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8881 (mm-30)
REVERT: B   68 ASP cc_start: 0.8666 (t70) cc_final: 0.8239 (t0)
REVERT: C   63 ARG cc_start: 0.8264 (mmp-170) cc_final: 0.7897 (mmp-170)
REVERT: C   73 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8784 (tm-30)
REVERT: C   85 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.9062 (mt0)
REVERT: C   94 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8609 (tm-30)
REVERT: C  105 GLU cc_start: 0.9144 (tp30) cc_final: 0.8750 (mm-30)
REVERT: C  107 THR cc_start: 0.9657 (m) cc_final: 0.9337 (t)
REVERT: C  128 ARG cc_start: 0.9126 (mtp85) cc_final: 0.8825 (mtp85)
REVERT: C  129 ARG cc_start: 0.9159 (tpp80) cc_final: 0.8785 (tpt-90)
REVERT: E   82 LEU cc_start: 0.9364 (tp) cc_final: 0.8985 (mm)
REVERT: E   85 GLN cc_start: 0.9368 (mt0) cc_final: 0.9110 (mt0)
REVERT: E   87 SER cc_start: 0.9486 (m) cc_final: 0.9195 (t)
REVERT: E  105 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8740 (mm-30)
REVERT: E  120 MET cc_start: 0.8727 (mmm) cc_final: 0.8111 (mmm)
REVERT: E  129 ARG cc_start: 0.8882 (mmm160) cc_final: 0.8274 (mmm160)
REVERT: F   35 ARG cc_start: 0.9380 (ttp80) cc_final: 0.8942 (ttm-80)
REVERT: F   44 LYS cc_start: 0.9519 (OUTLIER) cc_final: 0.9261 (mmmt)
REVERT: F   49 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.8947 (tp)
REVERT: F   74 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8980 (mm-30)
REVERT: F   79 LYS cc_start: 0.8994 (mtpp) cc_final: 0.8509 (mtmm)
REVERT: F   80 THR cc_start: 0.9517 (m) cc_final: 0.9103 (p)
REVERT: F   84 MET cc_start: 0.9001 (mmp) cc_final: 0.8773 (mmm)
REVERT: F   93 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8125 (tm-30)
REVERT: G   90 MET cc_start: 0.9112 (tmm) cc_final: 0.8803 (tpp)
REVERT: G  120 MET cc_start: 0.9324 (mmm) cc_final: 0.8761 (mtt)
REVERT: G  123 ASP cc_start: 0.7981 (m-30) cc_final: 0.7542 (t70)
REVERT: G  131 ARG cc_start: 0.8927 (mtp-110) cc_final: 0.8719 (mtp85)
REVERT: H   29 ILE cc_start: 0.8459 (mm) cc_final: 0.7822 (tp)
REVERT: H   53 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8601 (mt-10)
  outliers start: 20
  outliers final: 15
  residues processed: 242
  average time/residue: 0.2999
  time to fit residues: 90.8976
Evaluate side-chains
  250 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 231
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   85 GLN
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  124 ILE
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  105 GLU
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   44 LYS
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue  124 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 56 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 64 optimal weight:   10.0000
   chunk 8 optimal weight:    2.9990
   chunk 51 optimal weight:   10.0000
   chunk 57 optimal weight:    7.9990
   chunk 50 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9990
   chunk 70 optimal weight:    6.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 125 GLN
** D  75 HIS ** 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 = 0.3501 r_free = 0.3501 target = 0.052849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.036654 restraints weight = 56944.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.037733 restraints weight = 29959.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.038427 restraints weight = 20538.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.5564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049   9362  Z= 0.386
  Angle     :  0.851  17.302  13488  Z= 0.460
  Chirality :  0.042   0.299   1549
  Planarity :  0.005   0.072   1004
  Dihedral  : 31.309 158.155   2840
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 22.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 38.46 %
    Favored  : 57.09 %
  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:  1.43 (0.34), residues: 563
  helix:  1.46 (0.23), residues: 461
  sheet:  None (None), residues: 0
  loop : -1.26 (0.52), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 113 
 PHE   0.025   0.003   PHE G  67 
 TYR   0.015   0.002   TYR A  99 
 ARG   0.007   0.001   ARG G 128 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3454.32 seconds
wall clock time: 62 minutes 8.28 seconds (3728.28 seconds total)