Starting phenix.real_space_refine
on Tue Mar  3 20:31:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y5w_33627/03_2026/7y5w_33627.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y5w_33627/03_2026/7y5w_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y5w_33627/03_2026/7y5w_33627.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y5w_33627/03_2026/7y5w_33627.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y5w_33627/03_2026/7y5w_33627.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y5w_33627/03_2026/7y5w_33627.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.017
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.02, per 1000 atoms: 0.23
  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: 0.84
  Conformation dependent library (CDL) restraints added in 196.6 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: 1.51
  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: 1.57

  Time building geometry restraints manager: 1.05 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:             1.080
  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:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.530
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.240
-------------------------------------------------------------------------------
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= 0.151
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.006   0.000   ARG A 129 
 TYR   0.008   0.001   TYR B  51 
 PHE   0.007   0.001   PHE E  67 
 HIS   0.003   0.001   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9362)
  covalent geometry    : angle       0.53326 (13488)
  hydrogen bonds       : bond        0.09757 (  580)
  hydrogen bonds       : angle       3.60096 ( 1477)

*********************** 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  : 0.236 
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: 0.6597 (t70) cc_final: 0.6280 (t0)
REVERT: E   60 LEU cc_start: 0.7307 (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: 0.1405
  time to fit residues: 56.3208
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  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    0.0980
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:   10.0000
   chunk 74 optimal weight:    9.9990
   overall best weight:    2.5584

-------------------------------------------------------------------------------
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
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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.056167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.039709 restraints weight = 56026.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.041056 restraints weight = 26856.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.041901 restraints weight = 17667.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.042405 restraints weight = 13829.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.042670 restraints weight = 12032.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.3245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   9362  Z= 0.244
  Angle     :  0.694  11.561  13488  Z= 0.390
  Chirality :  0.039   0.257   1549
  Planarity :  0.005   0.054   1004
  Dihedral  : 30.838 147.511   2840
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 18.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 25.51 %
    Favored  : 68.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.16 (0.34), residues: 563
  helix:  1.89 (0.24), residues: 463
  sheet:  None (None), residues: 0
  loop : -0.70 (0.53), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E  83 
 TYR   0.018   0.002   TYR H  88 
 PHE   0.024   0.002   PHE H  61 
 HIS   0.005   0.002   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 ( 9362)
  covalent geometry    : angle       0.69392 (13488)
  hydrogen bonds       : bond        0.06295 (  580)
  hydrogen bonds       : angle       3.49749 ( 1477)

*********************** 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
  283 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 255
  time to evaluate  : 0.230 
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: 0.9691 (mt0) cc_final: 0.9262 (mm-40)
REVERT: A   90 MET cc_start: 0.8714 (tmm) cc_final: 0.8381 (tmm)
REVERT: A   94 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8792 (tm-30)
REVERT: A  112 ILE cc_start: 0.9723 (tp) cc_final: 0.9426 (pt)
REVERT: A  120 MET cc_start: 0.8691 (mtm) cc_final: 0.8229 (mtm)
REVERT: A  134 ARG cc_start: 0.8820 (tpp-160) cc_final: 0.8447 (tpp-160)
REVERT: B   44 LYS cc_start: 0.9116 (mmmt) cc_final: 0.8914 (mmmt)
REVERT: B   63 GLU cc_start: 0.9333 (mt-10) cc_final: 0.9025 (mm-30)
REVERT: B   68 ASP cc_start: 0.8605 (t70) cc_final: 0.8254 (t0)
REVERT: C   73 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8602 (tm-30)
REVERT: C   77 ASP cc_start: 0.9039 (t70) cc_final: 0.8783 (t0)
REVERT: C   85 GLN cc_start: 0.9320 (OUTLIER) cc_final: 0.9073 (mt0)
REVERT: C   94 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8541 (tm-30)
REVERT: C  128 ARG cc_start: 0.9443 (mtp85) cc_final: 0.9155 (mtp85)
REVERT: C  129 ARG cc_start: 0.9289 (tpp80) cc_final: 0.9054 (tpp80)
REVERT: D   44 LYS cc_start: 0.9344 (ttmm) cc_final: 0.9036 (mtpp)
REVERT: E   62 ILE cc_start: 0.8751 (mt) cc_final: 0.8249 (mt)
REVERT: F   44 LYS cc_start: 0.9540 (OUTLIER) cc_final: 0.9236 (mmmm)
REVERT: F   79 LYS cc_start: 0.9086 (mtpp) cc_final: 0.8557 (mtmm)
REVERT: F   80 THR cc_start: 0.9363 (m) cc_final: 0.8905 (p)
REVERT: F   92 ARG cc_start: 0.8954 (tmt-80) cc_final: 0.8747 (tmt170)
REVERT: G  120 MET cc_start: 0.8599 (mmm) cc_final: 0.8372 (mmm)
REVERT: G  131 ARG cc_start: 0.8962 (mtp85) cc_final: 0.8624 (mtp85)
REVERT: H   43 VAL cc_start: 0.8374 (t) cc_final: 0.8057 (t)
REVERT: H   49 LEU cc_start: 0.8378 (mp) cc_final: 0.8075 (mm)
REVERT: H   53 GLU cc_start: 0.9425 (mt-10) cc_final: 0.9177 (mt-10)
  outliers start: 28
  outliers final: 21
  residues processed: 262
  average time/residue: 0.1283
  time to fit residues: 42.6873
Evaluate side-chains
  253 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 230
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
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   60 VAL
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   68 GLN
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 E residue   65 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   87 SER
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 G residue  130 ILE
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 21 optimal weight:    0.8980
   chunk 70 optimal weight:    4.9990
   chunk 74 optimal weight:   10.0000
   chunk 69 optimal weight:    4.9990
   chunk 51 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 73 optimal weight:    6.9990
   chunk 10 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 55 optimal weight:    8.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
E  93 GLN
F  75 HIS
G  68 GLN
H  64 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.057967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.041295 restraints weight = 53395.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.042603 restraints weight = 25811.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.043418 restraints weight = 17070.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.043945 restraints weight = 13422.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.044189 restraints weight = 11658.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.3512

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= 0.170
  Angle     :  0.664   9.888  13488  Z= 0.373
  Chirality :  0.036   0.169   1549
  Planarity :  0.004   0.044   1004
  Dihedral  : 30.733 149.771   2840
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 17.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 28.74 %
    Favored  : 65.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.03 (0.35), residues: 563
  helix:  1.83 (0.24), residues: 462
  sheet:  None (None), residues: 0
  loop : -0.91 (0.52), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  67 
 TYR   0.010   0.002   TYR H  88 
 PHE   0.018   0.002   PHE H  61 
 HIS   0.004   0.001   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 9362)
  covalent geometry    : angle       0.66434 (13488)
  hydrogen bonds       : bond        0.05498 (  580)
  hydrogen bonds       : angle       3.30097 ( 1477)

*********************** 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
  285 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 257
  time to evaluate  : 0.243 
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   68 GLN cc_start: 0.9659 (mt0) cc_final: 0.9248 (mm-40)
REVERT: A   82 LEU cc_start: 0.8118 (mt) cc_final: 0.7473 (mt)
REVERT: A   90 MET cc_start: 0.8732 (tmm) cc_final: 0.8221 (tmm)
REVERT: A   97 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8480 (mm-30)
REVERT: A  112 ILE cc_start: 0.9701 (tp) cc_final: 0.9444 (pt)
REVERT: A  120 MET cc_start: 0.8693 (mtm) cc_final: 0.8314 (mtm)
REVERT: A  125 GLN cc_start: 0.9316 (mt0) cc_final: 0.8985 (mm-40)
REVERT: B   44 LYS cc_start: 0.9085 (mmmt) cc_final: 0.8830 (mmmt)
REVERT: B   63 GLU cc_start: 0.9303 (mt-10) cc_final: 0.9056 (mm-30)
REVERT: B   68 ASP cc_start: 0.8459 (t70) cc_final: 0.8157 (t0)
REVERT: C   77 ASP cc_start: 0.8996 (t70) cc_final: 0.8717 (t0)
REVERT: C   94 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8412 (tm-30)
REVERT: C  105 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8839 (mm-30)
REVERT: C  125 GLN cc_start: 0.9227 (mt0) cc_final: 0.8968 (mp10)
REVERT: C  129 ARG cc_start: 0.9206 (tpp80) cc_final: 0.8817 (tpp80)
REVERT: E   90 MET cc_start: 0.8940 (tpp) cc_final: 0.8732 (mmp)
REVERT: E   94 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8749 (mm-30)
REVERT: E  115 LYS cc_start: 0.9644 (mmmm) cc_final: 0.9363 (mmmm)
REVERT: E  120 MET cc_start: 0.8251 (mmm) cc_final: 0.7862 (mmm)
REVERT: E  122 LYS cc_start: 0.9567 (mtmt) cc_final: 0.9350 (ptpt)
REVERT: E  125 GLN cc_start: 0.9454 (mm110) cc_final: 0.9030 (mm110)
REVERT: E  129 ARG cc_start: 0.9072 (mmm160) cc_final: 0.8518 (mmm160)
REVERT: F   24 ASP cc_start: 0.8932 (p0) cc_final: 0.8726 (p0)
REVERT: F   25 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8685 (t0)
REVERT: F   31 LYS cc_start: 0.9355 (ttpp) cc_final: 0.9128 (ttmm)
REVERT: F   44 LYS cc_start: 0.9493 (OUTLIER) cc_final: 0.9236 (mmmm)
REVERT: F   79 LYS cc_start: 0.9056 (mtpp) cc_final: 0.8538 (mtmm)
REVERT: F   80 THR cc_start: 0.9417 (m) cc_final: 0.8806 (p)
REVERT: G   63 ARG cc_start: 0.9335 (tpt170) cc_final: 0.9123 (ttp-110)
REVERT: G   90 MET cc_start: 0.9024 (tmm) cc_final: 0.8751 (tpp)
REVERT: G  131 ARG cc_start: 0.9027 (mtp85) cc_final: 0.8671 (mtp85)
REVERT: H   49 LEU cc_start: 0.8147 (mp) cc_final: 0.7907 (mm)
REVERT: H   53 GLU cc_start: 0.9411 (mt-10) cc_final: 0.9154 (mt-10)
  outliers start: 28
  outliers final: 16
  residues processed: 264
  average time/residue: 0.1293
  time to fit residues: 43.0059
Evaluate side-chains
  254 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 236
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
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  109 LEU
Chi-restraints excluded: chain C residue  124 ILE
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   44 LYS
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   59 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 17 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   chunk 42 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.057185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.040965 restraints weight = 55137.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.042234 restraints weight = 26642.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.043046 restraints weight = 17594.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.043498 restraints weight = 13801.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.043810 restraints weight = 12073.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.3903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9362  Z= 0.173
  Angle     :  0.664  11.292  13488  Z= 0.373
  Chirality :  0.035   0.167   1549
  Planarity :  0.004   0.041   1004
  Dihedral  : 30.692 151.489   2840
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 16.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  6.68 %
    Allowed  : 27.53 %
    Favored  : 65.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.34), residues: 563
  helix:  1.72 (0.24), residues: 465
  sheet:  None (None), residues: 0
  loop : -0.66 (0.52), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  67 
 TYR   0.013   0.001   TYR A  99 
 PHE   0.011   0.001   PHE H  61 
 HIS   0.005   0.001   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 9362)
  covalent geometry    : angle       0.66393 (13488)
  hydrogen bonds       : bond        0.05487 (  580)
  hydrogen bonds       : angle       3.26577 ( 1477)

*********************** 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
  278 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 245
  time to evaluate  : 0.227 
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   90 MET cc_start: 0.8721 (tmm) cc_final: 0.8292 (tmm)
REVERT: A   97 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8571 (mm-30)
REVERT: A  112 ILE cc_start: 0.9692 (tp) cc_final: 0.9392 (pt)
REVERT: A  120 MET cc_start: 0.8750 (mtm) cc_final: 0.8162 (mtm)
REVERT: A  125 GLN cc_start: 0.9321 (mt0) cc_final: 0.8944 (mm-40)
REVERT: A  128 ARG cc_start: 0.9087 (mtp180) cc_final: 0.8827 (mtp-110)
REVERT: B   44 LYS cc_start: 0.9005 (mmmt) cc_final: 0.8572 (mmmt)
REVERT: B   68 ASP cc_start: 0.8458 (t70) cc_final: 0.8145 (t0)
REVERT: C   61 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7516 (mp)
REVERT: C   63 ARG cc_start: 0.8049 (mmp-170) cc_final: 0.7834 (mmp-170)
REVERT: C   73 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8662 (tm-30)
REVERT: C   77 ASP cc_start: 0.8982 (t70) cc_final: 0.8695 (t0)
REVERT: C   85 GLN cc_start: 0.9295 (OUTLIER) cc_final: 0.9048 (mt0)
REVERT: C   94 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8405 (tm-30)
REVERT: C  105 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8839 (mm-30)
REVERT: C  120 MET cc_start: 0.8907 (mmm) cc_final: 0.8495 (mmm)
REVERT: C  125 GLN cc_start: 0.9284 (mt0) cc_final: 0.8973 (mp10)
REVERT: C  129 ARG cc_start: 0.9183 (tpp80) cc_final: 0.8788 (ttp80)
REVERT: D   68 ASP cc_start: 0.9166 (m-30) cc_final: 0.8943 (m-30)
REVERT: D   92 ARG cc_start: 0.8693 (tpp80) cc_final: 0.8200 (ttp80)
REVERT: D   95 ARG cc_start: 0.5420 (mmp-170) cc_final: 0.5151 (mmp80)
REVERT: E   90 MET cc_start: 0.8924 (tpp) cc_final: 0.8683 (mmp)
REVERT: E   94 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8717 (mm-30)
REVERT: E  115 LYS cc_start: 0.9632 (mmmm) cc_final: 0.9378 (mmmm)
REVERT: E  120 MET cc_start: 0.8504 (mmm) cc_final: 0.8034 (mmm)
REVERT: E  122 LYS cc_start: 0.9570 (mtmt) cc_final: 0.9351 (ptpt)
REVERT: E  129 ARG cc_start: 0.9013 (mmm160) cc_final: 0.8692 (mmm160)
REVERT: F   23 ARG cc_start: 0.7779 (ptm160) cc_final: 0.7558 (ptm-80)
REVERT: F   31 LYS cc_start: 0.9338 (ttpp) cc_final: 0.9079 (ttmm)
REVERT: F   35 ARG cc_start: 0.9376 (ttp80) cc_final: 0.8828 (ttm-80)
REVERT: F   44 LYS cc_start: 0.9514 (OUTLIER) cc_final: 0.9252 (mmmm)
REVERT: F   74 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8801 (mm-30)
REVERT: F   79 LYS cc_start: 0.9057 (mtpp) cc_final: 0.8530 (mtmm)
REVERT: F   80 THR cc_start: 0.9384 (m) cc_final: 0.8783 (p)
REVERT: F   84 MET cc_start: 0.9091 (tpp) cc_final: 0.8845 (mmm)
REVERT: F   92 ARG cc_start: 0.9077 (tmt-80) cc_final: 0.8323 (tmt-80)
REVERT: F   93 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8252 (tm-30)
REVERT: G   63 ARG cc_start: 0.9333 (tpt170) cc_final: 0.8944 (ttp-110)
REVERT: G   90 MET cc_start: 0.8985 (tmm) cc_final: 0.8678 (tmm)
REVERT: G  131 ARG cc_start: 0.8975 (mtp85) cc_final: 0.8546 (mtp85)
REVERT: H   49 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7963 (mm)
REVERT: H   53 GLU cc_start: 0.9289 (mt-10) cc_final: 0.8976 (mt-10)
  outliers start: 33
  outliers final: 17
  residues processed: 254
  average time/residue: 0.1320
  time to fit residues: 42.2168
Evaluate side-chains
  256 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 235
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   61 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   29 ILE
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   62 LEU
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   86 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   61 LEU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 64 optimal weight:    7.9990
   chunk 5 optimal weight:    0.3980
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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**
F  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.058025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.041622 restraints weight = 55433.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.042889 restraints weight = 27506.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.043719 restraints weight = 18444.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.044229 restraints weight = 14489.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.044487 restraints weight = 12598.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.4077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9362  Z= 0.166
  Angle     :  0.661  11.344  13488  Z= 0.371
  Chirality :  0.035   0.163   1549
  Planarity :  0.004   0.041   1004
  Dihedral  : 30.638 152.770   2840
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 15.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  6.68 %
    Allowed  : 29.96 %
    Favored  : 63.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.96 (0.34), residues: 563
  helix:  1.74 (0.24), residues: 464
  sheet:  None (None), residues: 0
  loop : -0.69 (0.50), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  69 
 TYR   0.014   0.001   TYR H  88 
 PHE   0.013   0.001   PHE H  61 
 HIS   0.004   0.001   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 9362)
  covalent geometry    : angle       0.66056 (13488)
  hydrogen bonds       : bond        0.05391 (  580)
  hydrogen bonds       : angle       3.25624 ( 1477)

*********************** 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
  273 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 240
  time to evaluate  : 0.162 
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   68 GLN cc_start: 0.9661 (mt0) cc_final: 0.8800 (tp-100)
REVERT: A   84 PHE cc_start: 0.8944 (m-80) cc_final: 0.8637 (m-10)
REVERT: A   90 MET cc_start: 0.8734 (tmm) cc_final: 0.8239 (tmm)
REVERT: A  112 ILE cc_start: 0.9678 (tp) cc_final: 0.9385 (pt)
REVERT: A  120 MET cc_start: 0.8679 (mtm) cc_final: 0.8172 (mtm)
REVERT: A  125 GLN cc_start: 0.9297 (mt0) cc_final: 0.8968 (mm-40)
REVERT: A  128 ARG cc_start: 0.9106 (mtp180) cc_final: 0.8872 (mtp-110)
REVERT: B   44 LYS cc_start: 0.9136 (mmmt) cc_final: 0.8733 (mmmt)
REVERT: B   63 GLU cc_start: 0.9269 (mm-30) cc_final: 0.8954 (mm-30)
REVERT: B   68 ASP cc_start: 0.8478 (t70) cc_final: 0.8149 (t0)
REVERT: C   61 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7566 (mp)
REVERT: C   73 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8680 (tm-30)
REVERT: C   77 ASP cc_start: 0.8972 (t70) cc_final: 0.8679 (t0)
REVERT: C   85 GLN cc_start: 0.9289 (OUTLIER) cc_final: 0.9048 (mt0)
REVERT: C   94 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8354 (tm-30)
REVERT: C  105 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8750 (mm-30)
REVERT: C  125 GLN cc_start: 0.9260 (mt0) cc_final: 0.8964 (mp10)
REVERT: C  128 ARG cc_start: 0.9162 (mtp85) cc_final: 0.8945 (mtp85)
REVERT: C  129 ARG cc_start: 0.9125 (tpp80) cc_final: 0.8860 (ttp-110)
REVERT: D   68 ASP cc_start: 0.9107 (m-30) cc_final: 0.8905 (m-30)
REVERT: D   92 ARG cc_start: 0.8561 (tpp80) cc_final: 0.8272 (ttp80)
REVERT: E   90 MET cc_start: 0.8870 (tpp) cc_final: 0.8641 (mmp)
REVERT: E   94 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8665 (mm-30)
REVERT: E  115 LYS cc_start: 0.9627 (mmmm) cc_final: 0.9387 (mmmm)
REVERT: E  120 MET cc_start: 0.8599 (mmm) cc_final: 0.7914 (mmm)
REVERT: E  129 ARG cc_start: 0.8982 (mmm160) cc_final: 0.8471 (mmm160)
REVERT: F   23 ARG cc_start: 0.8148 (ptm160) cc_final: 0.7167 (ptm160)
REVERT: F   31 LYS cc_start: 0.9359 (ttpp) cc_final: 0.9099 (ttmm)
REVERT: F   35 ARG cc_start: 0.9373 (ttp80) cc_final: 0.8865 (ttm-80)
REVERT: F   44 LYS cc_start: 0.9487 (OUTLIER) cc_final: 0.9246 (mmmm)
REVERT: F   53 GLU cc_start: 0.9360 (tp30) cc_final: 0.9134 (tp30)
REVERT: F   74 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8789 (mm-30)
REVERT: F   79 LYS cc_start: 0.9096 (mtpp) cc_final: 0.8550 (mtmm)
REVERT: F   80 THR cc_start: 0.9423 (m) cc_final: 0.8763 (p)
REVERT: F   84 MET cc_start: 0.9096 (tpp) cc_final: 0.8849 (mmm)
REVERT: F   92 ARG cc_start: 0.9054 (tmt-80) cc_final: 0.8402 (tmt-80)
REVERT: F   93 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8206 (tm-30)
REVERT: G   63 ARG cc_start: 0.9359 (tpt170) cc_final: 0.8970 (ttp-110)
REVERT: G   69 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7694 (ppt170)
REVERT: G   70 LEU cc_start: 0.9289 (mt) cc_final: 0.8798 (mt)
REVERT: G   90 MET cc_start: 0.8997 (tmm) cc_final: 0.8649 (tmm)
REVERT: G  131 ARG cc_start: 0.8955 (mtp85) cc_final: 0.8625 (mtp85)
REVERT: H   36 ARG cc_start: 0.9172 (ptt-90) cc_final: 0.8937 (ptt-90)
REVERT: H   49 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7950 (mm)
REVERT: H   53 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8927 (mt-10)
  outliers start: 33
  outliers final: 21
  residues processed: 251
  average time/residue: 0.1377
  time to fit residues: 43.2750
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  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 LEU
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   62 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   92 LEU
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   69 ARG
Chi-restraints excluded: chain G residue  113 HIS
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 34 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 70 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 13 optimal weight:    5.9990
   overall best weight:    1.3988

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.056700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.040380 restraints weight = 57240.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.041645 restraints weight = 28927.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.042455 restraints weight = 19504.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.042948 restraints weight = 15361.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.043215 restraints weight = 13369.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.4359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9362  Z= 0.185
  Angle     :  0.679  11.117  13488  Z= 0.379
  Chirality :  0.036   0.165   1549
  Planarity :  0.004   0.044   1004
  Dihedral  : 30.707 154.241   2840
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 16.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  6.68 %
    Allowed  : 32.19 %
    Favored  : 61.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.99 (0.34), residues: 563
  helix:  1.85 (0.24), residues: 461
  sheet:  None (None), residues: 0
  loop : -1.11 (0.48), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  95 
 TYR   0.014   0.001   TYR H  88 
 PHE   0.011   0.001   PHE G  84 
 HIS   0.004   0.001   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 9362)
  covalent geometry    : angle       0.67940 (13488)
  hydrogen bonds       : bond        0.05556 (  580)
  hydrogen bonds       : angle       3.27168 ( 1477)

*********************** 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
  265 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 232
  time to evaluate  : 0.259 
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   90 MET cc_start: 0.8737 (tmm) cc_final: 0.8227 (tmm)
REVERT: A  112 ILE cc_start: 0.9697 (tp) cc_final: 0.9400 (pt)
REVERT: A  120 MET cc_start: 0.8700 (mtm) cc_final: 0.8243 (mtm)
REVERT: A  125 GLN cc_start: 0.9330 (mt0) cc_final: 0.9070 (mm-40)
REVERT: A  128 ARG cc_start: 0.9098 (mtp180) cc_final: 0.8454 (mtp-110)
REVERT: B   44 LYS cc_start: 0.9148 (mmmt) cc_final: 0.8728 (mmmt)
REVERT: B   53 GLU cc_start: 0.9342 (tp30) cc_final: 0.8990 (tp30)
REVERT: B   63 GLU cc_start: 0.9257 (mm-30) cc_final: 0.9033 (mm-30)
REVERT: B   68 ASP cc_start: 0.8549 (t70) cc_final: 0.8103 (t0)
REVERT: C   63 ARG cc_start: 0.8155 (mmp-170) cc_final: 0.7929 (mmp-170)
REVERT: C   73 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8696 (tm-30)
REVERT: C   77 ASP cc_start: 0.9013 (t70) cc_final: 0.8721 (t0)
REVERT: C   85 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.9018 (mt0)
REVERT: C   94 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8386 (tm-30)
REVERT: C  105 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8900 (mm-30)
REVERT: C  125 GLN cc_start: 0.9272 (mt0) cc_final: 0.8982 (mp10)
REVERT: C  129 ARG cc_start: 0.9186 (tpp80) cc_final: 0.8778 (ttp80)
REVERT: D   92 ARG cc_start: 0.8550 (tpp80) cc_final: 0.8232 (ttp80)
REVERT: E   79 LYS cc_start: 0.8402 (tptt) cc_final: 0.8114 (tptp)
REVERT: E   90 MET cc_start: 0.8912 (tpp) cc_final: 0.8662 (mmp)
REVERT: E   94 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8646 (mm-30)
REVERT: E  115 LYS cc_start: 0.9637 (mmmm) cc_final: 0.9391 (mmmm)
REVERT: E  129 ARG cc_start: 0.9008 (mmm160) cc_final: 0.8454 (mmm160)
REVERT: F   31 LYS cc_start: 0.9368 (ttpp) cc_final: 0.9106 (ttmm)
REVERT: F   35 ARG cc_start: 0.9384 (ttp80) cc_final: 0.8893 (ttm-80)
REVERT: F   44 LYS cc_start: 0.9517 (OUTLIER) cc_final: 0.9260 (mmmm)
REVERT: F   74 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8754 (mm-30)
REVERT: F   79 LYS cc_start: 0.9066 (mtpp) cc_final: 0.8532 (mtmm)
REVERT: F   80 THR cc_start: 0.9424 (m) cc_final: 0.8875 (p)
REVERT: F   84 MET cc_start: 0.9119 (tpp) cc_final: 0.8870 (mmm)
REVERT: F   92 ARG cc_start: 0.9078 (tmt-80) cc_final: 0.8395 (tmt-80)
REVERT: F   93 GLN cc_start: 0.8647 (tm-30) cc_final: 0.8237 (tm-30)
REVERT: G   63 ARG cc_start: 0.9384 (tpt170) cc_final: 0.8915 (ttp-110)
REVERT: G   90 MET cc_start: 0.9021 (tmm) cc_final: 0.8737 (tmm)
REVERT: G  123 ASP cc_start: 0.7936 (m-30) cc_final: 0.7503 (t70)
REVERT: G  131 ARG cc_start: 0.8926 (mtp85) cc_final: 0.8533 (mtp85)
REVERT: H   36 ARG cc_start: 0.9204 (ptt-90) cc_final: 0.8982 (ptt-90)
REVERT: H   49 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7946 (mm)
REVERT: H   53 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8900 (mt-10)
  outliers start: 33
  outliers final: 25
  residues processed: 243
  average time/residue: 0.1386
  time to fit residues: 42.3068
Evaluate side-chains
  250 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 222
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
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 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  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 E residue   61 LEU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   92 LEU
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   69 ARG
Chi-restraints excluded: chain G residue  113 HIS
Chi-restraints excluded: chain G residue  124 ILE
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   49 LEU
Chi-restraints excluded: chain H residue   59 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 67 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 69 optimal weight:    5.9990
   chunk 51 optimal weight:    0.7980
   chunk 54 optimal weight:    0.4980
   chunk 59 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    1.4384

-------------------------------------------------------------------------------
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**
F  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.057123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.040454 restraints weight = 55039.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.041706 restraints weight = 27715.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.042528 restraints weight = 18647.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.043018 restraints weight = 14749.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.043329 restraints weight = 12885.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.4486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9362  Z= 0.189
  Angle     :  0.708  16.197  13488  Z= 0.388
  Chirality :  0.036   0.176   1549
  Planarity :  0.004   0.045   1004
  Dihedral  : 30.744 155.000   2840
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 16.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 32.79 %
    Favored  : 61.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.90 (0.34), residues: 563
  helix:  1.77 (0.24), residues: 460
  sheet:  None (None), residues: 0
  loop : -1.05 (0.49), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 128 
 TYR   0.016   0.002   TYR H  88 
 PHE   0.012   0.001   PHE G  84 
 HIS   0.004   0.001   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 9362)
  covalent geometry    : angle       0.70849 (13488)
  hydrogen bonds       : bond        0.05506 (  580)
  hydrogen bonds       : angle       3.33423 ( 1477)

*********************** 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
  264 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 234
  time to evaluate  : 0.241 
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   90 MET cc_start: 0.8709 (tmm) cc_final: 0.8180 (tmm)
REVERT: A  112 ILE cc_start: 0.9697 (tp) cc_final: 0.9405 (pt)
REVERT: A  120 MET cc_start: 0.8686 (mtm) cc_final: 0.8233 (mtm)
REVERT: A  125 GLN cc_start: 0.9294 (mt0) cc_final: 0.8968 (mm-40)
REVERT: A  128 ARG cc_start: 0.9096 (mtp180) cc_final: 0.8436 (mtp-110)
REVERT: B   44 LYS cc_start: 0.9151 (mmmt) cc_final: 0.8725 (mmmt)
REVERT: B   63 GLU cc_start: 0.9260 (mm-30) cc_final: 0.9052 (mm-30)
REVERT: B   68 ASP cc_start: 0.8399 (t70) cc_final: 0.8081 (t0)
REVERT: B   92 ARG cc_start: 0.8867 (ptm-80) cc_final: 0.8428 (ttp80)
REVERT: C   63 ARG cc_start: 0.8188 (mmp-170) cc_final: 0.7947 (mmp-170)
REVERT: C   73 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8709 (tm-30)
REVERT: C   77 ASP cc_start: 0.9031 (t70) cc_final: 0.8726 (t0)
REVERT: C   85 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.9010 (mt0)
REVERT: C   94 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8429 (tm-30)
REVERT: C  105 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8925 (mm-30)
REVERT: C  107 THR cc_start: 0.9658 (m) cc_final: 0.9281 (t)
REVERT: C  125 GLN cc_start: 0.9267 (mt0) cc_final: 0.8957 (mp10)
REVERT: C  129 ARG cc_start: 0.9165 (tpp80) cc_final: 0.8768 (ttp80)
REVERT: D   68 ASP cc_start: 0.9138 (m-30) cc_final: 0.8853 (m-30)
REVERT: D   92 ARG cc_start: 0.8470 (tpp80) cc_final: 0.8058 (ttp80)
REVERT: E   87 SER cc_start: 0.9530 (m) cc_final: 0.9192 (t)
REVERT: E   90 MET cc_start: 0.8905 (tpp) cc_final: 0.8655 (mmp)
REVERT: E   94 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8629 (mm-30)
REVERT: E  115 LYS cc_start: 0.9635 (mmmm) cc_final: 0.9374 (mmmm)
REVERT: E  120 MET cc_start: 0.8724 (mmm) cc_final: 0.7966 (mmm)
REVERT: E  128 ARG cc_start: 0.9425 (mmm-85) cc_final: 0.9193 (mmm-85)
REVERT: E  129 ARG cc_start: 0.8997 (mmm160) cc_final: 0.8598 (mmm160)
REVERT: F   23 ARG cc_start: 0.7555 (ptm160) cc_final: 0.6833 (ptm160)
REVERT: F   31 LYS cc_start: 0.9373 (ttpp) cc_final: 0.9108 (ttmm)
REVERT: F   35 ARG cc_start: 0.9389 (ttp80) cc_final: 0.8904 (ttm-80)
REVERT: F   44 LYS cc_start: 0.9528 (OUTLIER) cc_final: 0.9270 (mmmt)
REVERT: F   49 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.8909 (tp)
REVERT: F   74 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8790 (mm-30)
REVERT: F   79 LYS cc_start: 0.9065 (mtpp) cc_final: 0.8530 (mtmm)
REVERT: F   80 THR cc_start: 0.9426 (m) cc_final: 0.8855 (p)
REVERT: F   84 MET cc_start: 0.9126 (tpp) cc_final: 0.8873 (mmm)
REVERT: F   92 ARG cc_start: 0.9072 (tmt-80) cc_final: 0.8371 (tmt-80)
REVERT: F   93 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8246 (tm-30)
REVERT: G   69 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7891 (ppt170)
REVERT: G   90 MET cc_start: 0.9069 (tmm) cc_final: 0.8781 (tmm)
REVERT: G  123 ASP cc_start: 0.8052 (m-30) cc_final: 0.7541 (t70)
REVERT: H   49 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7988 (mm)
REVERT: H   53 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8917 (mt-10)
  outliers start: 30
  outliers final: 23
  residues processed: 243
  average time/residue: 0.1400
  time to fit residues: 42.5754
Evaluate side-chains
  253 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 225
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
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 B residue   86 VAL
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   29 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   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 F residue   90 LEU
Chi-restraints excluded: chain G residue   69 ARG
Chi-restraints excluded: chain G residue  113 HIS
Chi-restraints excluded: chain G residue  124 ILE
Chi-restraints excluded: chain H residue   49 LEU
Chi-restraints excluded: chain H residue   59 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 67 optimal weight:    4.9990
   chunk 72 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    2.1588

-------------------------------------------------------------------------------
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**
G  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.055789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.039167 restraints weight = 54509.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.040405 restraints weight = 27264.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.041159 restraints weight = 18298.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.041678 restraints weight = 14517.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.041921 restraints weight = 12661.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.4728

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= 0.224
  Angle     :  0.748  16.890  13488  Z= 0.408
  Chirality :  0.037   0.181   1549
  Planarity :  0.005   0.045   1004
  Dihedral  : 30.919 156.316   2840
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 18.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  7.49 %
    Allowed  : 33.60 %
    Favored  : 58.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.34), residues: 563
  helix:  1.75 (0.24), residues: 460
  sheet:  None (None), residues: 0
  loop : -1.06 (0.50), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  36 
 TYR   0.018   0.002   TYR A  99 
 PHE   0.015   0.002   PHE A  84 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00510 ( 9362)
  covalent geometry    : angle       0.74798 (13488)
  hydrogen bonds       : bond        0.05931 (  580)
  hydrogen bonds       : angle       3.46394 ( 1477)

*********************** 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
  260 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 223
  time to evaluate  : 0.251 
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   90 MET cc_start: 0.8701 (tmm) cc_final: 0.8176 (tmm)
REVERT: A  120 MET cc_start: 0.8680 (mtm) cc_final: 0.8258 (mtm)
REVERT: A  125 GLN cc_start: 0.9300 (mt0) cc_final: 0.8977 (mm-40)
REVERT: B   44 LYS cc_start: 0.9174 (mmmt) cc_final: 0.8753 (mmmt)
REVERT: B   63 GLU cc_start: 0.9269 (mm-30) cc_final: 0.9034 (mm-30)
REVERT: B   68 ASP cc_start: 0.8520 (t70) cc_final: 0.8079 (t0)
REVERT: B   92 ARG cc_start: 0.8825 (ptm-80) cc_final: 0.8525 (ttp80)
REVERT: C   63 ARG cc_start: 0.8255 (mmp-170) cc_final: 0.7954 (mmp-170)
REVERT: C   73 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8590 (tm-30)
REVERT: C   77 ASP cc_start: 0.9060 (t70) cc_final: 0.8778 (t0)
REVERT: C   85 GLN cc_start: 0.9271 (OUTLIER) cc_final: 0.8909 (mt0)
REVERT: C   94 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8433 (tm-30)
REVERT: C  105 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8901 (mm-30)
REVERT: C  125 GLN cc_start: 0.9240 (mt0) cc_final: 0.8896 (mp10)
REVERT: D   79 LYS cc_start: 0.8884 (mmtt) cc_final: 0.8578 (mmmm)
REVERT: E   79 LYS cc_start: 0.8499 (tptt) cc_final: 0.8043 (tptp)
REVERT: E   82 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8960 (mm)
REVERT: E   87 SER cc_start: 0.9562 (OUTLIER) cc_final: 0.9228 (t)
REVERT: E   90 MET cc_start: 0.8908 (tpp) cc_final: 0.8692 (mmp)
REVERT: E  105 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8684 (mm-30)
REVERT: E  120 MET cc_start: 0.8614 (mmm) cc_final: 0.7905 (mmm)
REVERT: E  129 ARG cc_start: 0.9004 (mmm160) cc_final: 0.8607 (mmm160)
REVERT: F   31 LYS cc_start: 0.9389 (ttpp) cc_final: 0.9133 (ttmm)
REVERT: F   35 ARG cc_start: 0.9398 (ttp80) cc_final: 0.8915 (ttm-80)
REVERT: F   44 LYS cc_start: 0.9520 (OUTLIER) cc_final: 0.9277 (mmmt)
REVERT: F   49 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.8878 (tp)
REVERT: F   53 GLU cc_start: 0.9433 (tp30) cc_final: 0.9092 (tp30)
REVERT: F   79 LYS cc_start: 0.9055 (mtpp) cc_final: 0.8563 (mtmm)
REVERT: F   80 THR cc_start: 0.9461 (m) cc_final: 0.8905 (p)
REVERT: F   84 MET cc_start: 0.9121 (tpp) cc_final: 0.8888 (mmm)
REVERT: F   92 ARG cc_start: 0.9024 (tmt-80) cc_final: 0.8719 (ttt90)
REVERT: F   93 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8200 (tm-30)
REVERT: G   69 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.8005 (ppt170)
REVERT: G  109 LEU cc_start: 0.9170 (mm) cc_final: 0.8955 (mp)
REVERT: G  123 ASP cc_start: 0.8068 (m-30) cc_final: 0.7622 (t70)
REVERT: H   36 ARG cc_start: 0.9245 (ptt-90) cc_final: 0.9037 (ptt-90)
REVERT: H   49 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7932 (mm)
REVERT: H   53 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8909 (mt-10)
  outliers start: 37
  outliers final: 26
  residues processed: 234
  average time/residue: 0.1293
  time to fit residues: 38.1647
Evaluate side-chains
  253 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 220
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
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 B residue   86 VAL
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   29 ILE
Chi-restraints excluded: chain D residue   50 ILE
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   82 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue   89 VAL
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 F residue   90 LEU
Chi-restraints excluded: chain G residue   65 LEU
Chi-restraints excluded: chain G residue   69 ARG
Chi-restraints excluded: chain G residue   94 GLU
Chi-restraints excluded: chain G residue  113 HIS
Chi-restraints excluded: chain G residue  124 ILE
Chi-restraints excluded: chain H residue   49 LEU
Chi-restraints excluded: chain H residue   59 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 57 optimal weight:    7.9990
   chunk 52 optimal weight:    6.9990
   chunk 4 optimal weight:    0.5980
   chunk 74 optimal weight:   10.0000
   chunk 71 optimal weight:    6.9990
   chunk 47 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0670
   chunk 59 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    1.2920

-------------------------------------------------------------------------------
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**
G  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.056254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.039747 restraints weight = 54539.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.040981 restraints weight = 27469.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.041786 restraints weight = 18476.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.042285 restraints weight = 14592.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.042481 restraints weight = 12703.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.4868

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= 0.190
  Angle     :  0.767  17.657  13488  Z= 0.414
  Chirality :  0.037   0.196   1549
  Planarity :  0.005   0.046   1004
  Dihedral  : 30.858 156.503   2840
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 17.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 35.63 %
    Favored  : 58.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.79 (0.34), residues: 563
  helix:  1.69 (0.24), residues: 460
  sheet:  None (None), residues: 0
  loop : -1.04 (0.51), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  36 
 TYR   0.014   0.002   TYR H  72 
 PHE   0.019   0.002   PHE A  84 
 HIS   0.004   0.001   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 9362)
  covalent geometry    : angle       0.76671 (13488)
  hydrogen bonds       : bond        0.05521 (  580)
  hydrogen bonds       : angle       3.39115 ( 1477)

*********************** 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
  262 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 232
  time to evaluate  : 0.247 
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   90 MET cc_start: 0.8675 (tmm) cc_final: 0.8171 (tmm)
REVERT: A  112 ILE cc_start: 0.9668 (tp) cc_final: 0.9439 (pt)
REVERT: A  120 MET cc_start: 0.8711 (mtm) cc_final: 0.8273 (mtm)
REVERT: A  125 GLN cc_start: 0.9276 (mt0) cc_final: 0.8948 (mm-40)
REVERT: A  128 ARG cc_start: 0.9123 (mtm110) cc_final: 0.8836 (mtp-110)
REVERT: B   44 LYS cc_start: 0.9165 (mmmt) cc_final: 0.8739 (mmmt)
REVERT: B   63 GLU cc_start: 0.9258 (mm-30) cc_final: 0.9032 (mm-30)
REVERT: B   68 ASP cc_start: 0.8520 (t70) cc_final: 0.8117 (t0)
REVERT: B   92 ARG cc_start: 0.8800 (ptm-80) cc_final: 0.8502 (ttp80)
REVERT: C   63 ARG cc_start: 0.8185 (mmp-170) cc_final: 0.7854 (mmp-170)
REVERT: C   73 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8666 (tm-30)
REVERT: C   85 GLN cc_start: 0.9262 (OUTLIER) cc_final: 0.9004 (mt0)
REVERT: C   94 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8416 (tm-30)
REVERT: C  105 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8917 (mm-30)
REVERT: C  107 THR cc_start: 0.9669 (m) cc_final: 0.9331 (t)
REVERT: C  125 GLN cc_start: 0.9237 (mt0) cc_final: 0.8899 (mp10)
REVERT: C  129 ARG cc_start: 0.9195 (tpp80) cc_final: 0.8875 (tpp80)
REVERT: D   79 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8518 (mmmm)
REVERT: E   76 GLN cc_start: 0.9116 (pt0) cc_final: 0.8752 (pp30)
REVERT: E   79 LYS cc_start: 0.8512 (tptt) cc_final: 0.8003 (tptp)
REVERT: E   82 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8962 (mm)
REVERT: E   87 SER cc_start: 0.9532 (OUTLIER) cc_final: 0.9195 (t)
REVERT: E   90 MET cc_start: 0.8896 (tpp) cc_final: 0.8678 (mmp)
REVERT: E  105 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8691 (mm-30)
REVERT: E  120 MET cc_start: 0.8599 (mmm) cc_final: 0.7849 (mmm)
REVERT: E  129 ARG cc_start: 0.9013 (mmm160) cc_final: 0.8535 (mmm160)
REVERT: F   23 ARG cc_start: 0.7766 (ptm160) cc_final: 0.7333 (ptm160)
REVERT: F   31 LYS cc_start: 0.9371 (ttpp) cc_final: 0.9094 (ttmm)
REVERT: F   35 ARG cc_start: 0.9375 (ttp80) cc_final: 0.8913 (ttm-80)
REVERT: F   44 LYS cc_start: 0.9521 (OUTLIER) cc_final: 0.9271 (mmmt)
REVERT: F   49 LEU cc_start: 0.9437 (mm) cc_final: 0.8975 (tp)
REVERT: F   53 GLU cc_start: 0.9418 (tp30) cc_final: 0.9078 (tp30)
REVERT: F   74 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8702 (mm-30)
REVERT: F   79 LYS cc_start: 0.9054 (mtpp) cc_final: 0.8545 (mtmm)
REVERT: F   80 THR cc_start: 0.9434 (m) cc_final: 0.8862 (p)
REVERT: F   92 ARG cc_start: 0.9020 (tmt-80) cc_final: 0.8735 (ttt90)
REVERT: F   93 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8174 (tm-30)
REVERT: G   67 PHE cc_start: 0.9025 (t80) cc_final: 0.8346 (t80)
REVERT: G   69 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8141 (ppt170)
REVERT: G  123 ASP cc_start: 0.7998 (m-30) cc_final: 0.7627 (t70)
REVERT: G  131 ARG cc_start: 0.8925 (mtp-110) cc_final: 0.8614 (mtp85)
REVERT: H   49 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7835 (mm)
REVERT: H   53 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8799 (mt-10)
  outliers start: 30
  outliers final: 23
  residues processed: 242
  average time/residue: 0.1403
  time to fit residues: 42.3681
Evaluate side-chains
  254 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 225
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
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 B residue   81 VAL
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   29 ILE
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue   89 VAL
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   90 LEU
Chi-restraints excluded: chain G residue   69 ARG
Chi-restraints excluded: chain G residue  113 HIS
Chi-restraints excluded: chain G residue  124 ILE
Chi-restraints excluded: chain H residue   49 LEU
Chi-restraints excluded: chain H residue   59 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 71 optimal weight:    6.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** D  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 = 0.3564 r_free = 0.3564 target = 0.057325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.041203 restraints weight = 55377.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.042471 restraints weight = 27416.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.043293 restraints weight = 18253.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.043789 restraints weight = 14347.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.044085 restraints weight = 12457.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.5011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9362  Z= 0.179
  Angle     :  0.782  18.436  13488  Z= 0.418
  Chirality :  0.036   0.180   1549
  Planarity :  0.006   0.135   1004
  Dihedral  : 30.746 156.772   2840
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 17.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 37.04 %
    Favored  : 57.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.73 (0.34), residues: 563
  helix:  1.64 (0.23), residues: 460
  sheet:  None (None), residues: 0
  loop : -1.04 (0.51), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG H  67 
 TYR   0.016   0.002   TYR H  72 
 PHE   0.023   0.002   PHE G  78 
 HIS   0.004   0.001   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 9362)
  covalent geometry    : angle       0.78201 (13488)
  hydrogen bonds       : bond        0.05441 (  580)
  hydrogen bonds       : angle       3.41625 ( 1477)

********************** 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: 27
    poor density    : 231
  time to evaluate  : 0.243 
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   90 MET cc_start: 0.8665 (tmm) cc_final: 0.7399 (tmm)
REVERT: A  112 ILE cc_start: 0.9655 (tp) cc_final: 0.9422 (pt)
REVERT: A  120 MET cc_start: 0.8690 (mtm) cc_final: 0.8233 (mtm)
REVERT: A  125 GLN cc_start: 0.9265 (mt0) cc_final: 0.8933 (mm-40)
REVERT: A  128 ARG cc_start: 0.9063 (mtm110) cc_final: 0.8788 (mtp-110)
REVERT: B   44 LYS cc_start: 0.9129 (mmmt) cc_final: 0.8668 (mmmt)
REVERT: B   63 GLU cc_start: 0.9251 (mm-30) cc_final: 0.9015 (mm-30)
REVERT: B   68 ASP cc_start: 0.8509 (t70) cc_final: 0.8134 (t0)
REVERT: B   92 ARG cc_start: 0.8840 (ptm-80) cc_final: 0.8526 (ttp80)
REVERT: C   63 ARG cc_start: 0.8132 (mmp-170) cc_final: 0.7778 (mmp-170)
REVERT: C   73 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8740 (tm-30)
REVERT: C   85 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.8987 (mt0)
REVERT: C   94 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8375 (tm-30)
REVERT: C  105 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8902 (mm-30)
REVERT: C  107 THR cc_start: 0.9643 (m) cc_final: 0.9317 (t)
REVERT: C  125 GLN cc_start: 0.9254 (mt0) cc_final: 0.8930 (mp10)
REVERT: C  129 ARG cc_start: 0.9148 (tpp80) cc_final: 0.8902 (ttp-170)
REVERT: D   67 ARG cc_start: 0.8950 (ttm110) cc_final: 0.8328 (ttm-80)
REVERT: D   79 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8527 (mmmm)
REVERT: D   84 MET cc_start: 0.9168 (tpp) cc_final: 0.8681 (mmm)
REVERT: E   76 GLN cc_start: 0.9136 (pt0) cc_final: 0.8746 (pp30)
REVERT: E   79 LYS cc_start: 0.8466 (tptt) cc_final: 0.8037 (tptp)
REVERT: E   82 LEU cc_start: 0.9306 (tp) cc_final: 0.8950 (mm)
REVERT: E   87 SER cc_start: 0.9507 (OUTLIER) cc_final: 0.9175 (t)
REVERT: E  105 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8688 (mm-30)
REVERT: E  120 MET cc_start: 0.8478 (mmm) cc_final: 0.8191 (mmm)
REVERT: E  129 ARG cc_start: 0.9026 (mmm160) cc_final: 0.8574 (mmm160)
REVERT: F   23 ARG cc_start: 0.7807 (ptm160) cc_final: 0.7301 (ptm160)
REVERT: F   31 LYS cc_start: 0.9383 (ttpp) cc_final: 0.9113 (ttmm)
REVERT: F   35 ARG cc_start: 0.9346 (ttp80) cc_final: 0.8899 (ttm-80)
REVERT: F   44 LYS cc_start: 0.9551 (ttmm) cc_final: 0.9280 (mmmt)
REVERT: F   49 LEU cc_start: 0.9343 (mm) cc_final: 0.8951 (tp)
REVERT: F   79 LYS cc_start: 0.9039 (mtpp) cc_final: 0.8523 (mtmm)
REVERT: F   80 THR cc_start: 0.9410 (m) cc_final: 0.8846 (p)
REVERT: F   92 ARG cc_start: 0.9064 (tmt-80) cc_final: 0.8780 (ttt90)
REVERT: F   93 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8195 (tm-30)
REVERT: G   67 PHE cc_start: 0.8988 (t80) cc_final: 0.8362 (t80)
REVERT: G  123 ASP cc_start: 0.8018 (m-30) cc_final: 0.7719 (t70)
REVERT: G  125 GLN cc_start: 0.9658 (mm-40) cc_final: 0.9342 (mm-40)
REVERT: G  131 ARG cc_start: 0.8968 (mtp-110) cc_final: 0.8634 (mtp85)
REVERT: H   29 ILE cc_start: 0.8824 (mm) cc_final: 0.8460 (tp)
REVERT: H   53 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8717 (mt-10)
  outliers start: 27
  outliers final: 21
  residues processed: 240
  average time/residue: 0.1365
  time to fit residues: 41.1903
Evaluate side-chains
  251 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 228
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
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 B residue   81 VAL
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   29 ILE
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue   89 VAL
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 G residue  113 HIS
Chi-restraints excluded: chain G residue  124 ILE
Chi-restraints excluded: chain H residue   59 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 35 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 59 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   chunk 14 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
** D  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.056203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.039529 restraints weight = 54039.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.040772 restraints weight = 27198.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 70)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.041566 restraints weight = 18401.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.042015 restraints weight = 14566.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.042337 restraints weight = 12798.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.5095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9362  Z= 0.211
  Angle     :  0.816  18.674  13488  Z= 0.438
  Chirality :  0.038   0.280   1549
  Planarity :  0.006   0.126   1004
  Dihedral  : 30.790 156.878   2840
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 19.34
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.68 (0.35), residues: 563
  helix:  1.62 (0.24), residues: 460
  sheet:  None (None), residues: 0
  loop : -1.12 (0.52), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.026   0.001   ARG G  69 
 TYR   0.017   0.002   TYR H  72 
 PHE   0.019   0.002   PHE G  78 
 HIS   0.004   0.001   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 9362)
  covalent geometry    : angle       0.81568 (13488)
  hydrogen bonds       : bond        0.05772 (  580)
  hydrogen bonds       : angle       3.53196 ( 1477)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2115.10 seconds
wall clock time: 36 minutes 49.84 seconds (2209.84 seconds total)