Starting phenix.real_space_refine
on Mon Jul 28 10:36:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6m4d_30076/07_2025/6m4d_30076.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6m4d_30076/07_2025/6m4d_30076.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6m4d_30076/07_2025/6m4d_30076.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6m4d_30076/07_2025/6m4d_30076.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6m4d_30076/07_2025/6m4d_30076.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6m4d_30076/07_2025/6m4d_30076.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.006
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     250      5.49       5
     S      14      5.16       5
     C    5801      2.51       5
     N    1962      2.21       5
     O    2470      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10497
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 625
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
    Chain: "B"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 693
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    Chain: "D"
      Number of atoms: 730
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 730
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 2548
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 2548
          Classifications: {'DNA': 125}
          Link IDs: {'rna3p': 124}
    Chain: "J"
      Number of atoms: 2577
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 2577
          Classifications: {'DNA': 125}
          Link IDs: {'rna3p': 124}
  Restraints were copied for chains:
    E, F, G, H
  Time building chain proxies: 6.66, per 1000 atoms: 0.63
  Number of scatterers: 10497
  At special positions: 0
  Unit cell: (131.04, 79.04, 114.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P     250     15.00
     O    2470      8.00
     N    1962      7.00
     C    5801      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: 3.03
  Conformation dependent library (CDL) restraints added in 715.5 milliseconds
  

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1272

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 3 sheets defined
      75.1% alpha, 0.9% beta
      123 base pairs and 185 stacking pairs defined.
    Time for finding SS restraints: 4.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 77
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.724A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLY A 132 " --> pdb=" O   ARG A 128 " (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 50 through 76
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 18 through 24
    Processing helix  chain 'C' and resid 28 through 38
    Processing helix  chain 'C' and resid 47 through 75
    Processing helix  chain 'C' and resid 82 through 91
      removed outlier: 3.571A  pdb=" N   LEU C  86 " --> pdb=" O   THR C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 100
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
    Processing helix  chain 'E' and resid 63 through 77
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.723A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLY E 132 " --> pdb=" O   ARG E 128 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 50 through 76
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 18 through 24
    Processing helix  chain 'G' and resid 28 through 38
    Processing helix  chain 'G' and resid 47 through 75
    Processing helix  chain 'G' and resid 82 through 91
      removed outlier: 3.571A  pdb=" N   LEU G  86 " --> pdb=" O   THR G  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 93 through 100
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 123
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.952A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.068A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3

    381 hydrogen bonds defined for protein.
    1131 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      317 hydrogen bonds
      622 hydrogen bond angles
      0 basepair planarities
      123 basepair parallelities
      185 stacking parallelities
  Total time for adding SS restraints: 3.43

  Time building geometry restraints manager: 3.57 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1934
        1.33 -     1.45: 3674
        1.45 -     1.57: 5056
        1.57 -     1.68: 498
        1.68 -     1.80: 24
  Bond restraints: 11186
  Sorted by residual:
  bond pdb=" P    DG J 136 "
       pdb=" O5'  DG J 136 "
    ideal  model  delta    sigma   weight residual
    1.600  1.639 -0.039 2.00e-02 2.50e+03 3.89e+00
  bond pdb=" C3'  DC J 126 "
       pdb=" O3'  DC J 126 "
    ideal  model  delta    sigma   weight residual
    1.422  1.473 -0.051 3.00e-02 1.11e+03 2.85e+00
  bond pdb=" C5'  DG J 136 "
       pdb=" C4'  DG J 136 "
    ideal  model  delta    sigma   weight residual
    1.518  1.551 -0.033 2.00e-02 2.50e+03 2.66e+00
  bond pdb=" C1'  DC I  56 "
       pdb=" N1   DC I  56 "
    ideal  model  delta    sigma   weight residual
    1.490  1.441  0.049 3.00e-02 1.11e+03 2.62e+00
  bond pdb=" C3'  DT J 128 "
       pdb=" O3'  DT J 128 "
    ideal  model  delta    sigma   weight residual
    1.422  1.470 -0.048 3.00e-02 1.11e+03 2.59e+00
  ... (remaining 11181 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.78: 15964
        2.78 -     5.56: 196
        5.56 -     8.35: 7
        8.35 -    11.13: 5
       11.13 -    13.91: 1
  Bond angle restraints: 16173
  Sorted by residual:
  angle pdb=" O3'  DC J 135 "
        pdb=" P    DG J 136 "
        pdb=" O5'  DG J 136 "
      ideal   model   delta    sigma   weight residual
     104.00  117.91  -13.91 1.50e+00 4.44e-01 8.60e+01
  angle pdb=" C3'  DC J 135 "
        pdb=" O3'  DC J 135 "
        pdb=" P    DG J 136 "
      ideal   model   delta    sigma   weight residual
     120.20  131.11  -10.91 1.50e+00 4.44e-01 5.29e+01
  angle pdb=" P    DG J 136 "
        pdb=" O5'  DG J 136 "
        pdb=" C5'  DG J 136 "
      ideal   model   delta    sigma   weight residual
     120.00  125.98   -5.98 1.50e+00 4.44e-01 1.59e+01
  angle pdb=" C3'  DC I 111 "
        pdb=" C2'  DC I 111 "
        pdb=" C1'  DC I 111 "
      ideal   model   delta    sigma   weight residual
     101.60   96.35    5.25 1.50e+00 4.44e-01 1.23e+01
  angle pdb=" C5'  DG J 136 "
        pdb=" C4'  DG J 136 "
        pdb=" O4'  DG J 136 "
      ideal   model   delta    sigma   weight residual
     109.40  114.50   -5.10 1.50e+00 4.44e-01 1.16e+01
  ... (remaining 16168 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.98: 4628
       34.98 -    69.96: 1358
       69.96 -   104.94: 65
      104.94 -   139.92: 7
      139.92 -   174.90: 2
  Dihedral angle restraints: 6060
    sinusoidal: 4090
      harmonic: 1970
  Sorted by residual:
  dihedral pdb=" CA  PRO H 103 "
           pdb=" C   PRO H 103 "
           pdb=" N   GLY H 104 "
           pdb=" CA  GLY H 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.07   22.93     0      5.00e+00 4.00e-02 2.10e+01
  dihedral pdb=" CA  PRO D 103 "
           pdb=" C   PRO D 103 "
           pdb=" N   GLY D 104 "
           pdb=" CA  GLY D 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.08   22.92     0      5.00e+00 4.00e-02 2.10e+01
  dihedral pdb=" CA  LYS D  34 "
           pdb=" C   LYS D  34 "
           pdb=" N   GLU D  35 "
           pdb=" CA  GLU D  35 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.78  -22.22     0      5.00e+00 4.00e-02 1.98e+01
  ... (remaining 6057 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1609
       0.069 -    0.138: 218
       0.138 -    0.207: 19
       0.207 -    0.276: 3
       0.276 -    0.345: 1
  Chirality restraints: 1850
  Sorted by residual:
  chirality pdb=" C1'  DT J  13 "
            pdb=" O4'  DT J  13 "
            pdb=" C2'  DT J  13 "
            pdb=" N1   DT J  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.12    0.35 2.00e-01 2.50e+01 2.98e+00
  chirality pdb=" C1'  DG I  19 "
            pdb=" O4'  DG I  19 "
            pdb=" C2'  DG I  19 "
            pdb=" N9   DG I  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.17    0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" P    DG J 136 "
            pdb=" OP1  DG J 136 "
            pdb=" OP2  DG J 136 "
            pdb=" O5'  DG J 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.59   -0.24 2.00e-01 2.50e+01 1.49e+00
  ... (remaining 1847 not shown)

  Planarity restraints: 1178
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  13 "   -0.036 2.00e-02 2.50e+03   2.52e-02 1.91e+01
        pdb=" N9   DG I  13 "    0.069 2.00e-02 2.50e+03
        pdb=" C8   DG I  13 "   -0.030 2.00e-02 2.50e+03
        pdb=" N7   DG I  13 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DG I  13 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DG I  13 "    0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I  13 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1   DG I  13 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DG I  13 "    0.016 2.00e-02 2.50e+03
        pdb=" N2   DG I  13 "   -0.017 2.00e-02 2.50e+03
        pdb=" N3   DG I  13 "    0.000 2.00e-02 2.50e+03
        pdb=" C4   DG I  13 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA J  14 "    0.026 2.00e-02 2.50e+03   2.54e-02 1.78e+01
        pdb=" N9   DA J  14 "   -0.068 2.00e-02 2.50e+03
        pdb=" C8   DA J  14 "    0.040 2.00e-02 2.50e+03
        pdb=" N7   DA J  14 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5   DA J  14 "   -0.007 2.00e-02 2.50e+03
        pdb=" C6   DA J  14 "   -0.000 2.00e-02 2.50e+03
        pdb=" N6   DA J  14 "   -0.004 2.00e-02 2.50e+03
        pdb=" N1   DA J  14 "    0.015 2.00e-02 2.50e+03
        pdb=" C2   DA J  14 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DA J  14 "    0.000 2.00e-02 2.50e+03
        pdb=" C4   DA J  14 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C  72 "   -0.017 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        pdb=" C   ALA C  72 "    0.059 2.00e-02 2.50e+03
        pdb=" O   ALA C  72 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   SER C  73 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1175 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 352
        2.64 -     3.20: 10613
        3.20 -     3.77: 22149
        3.77 -     4.33: 26096
        4.33 -     4.90: 35636
  Nonbonded interactions: 94846
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG B  35 "
            pdb=" OP2  DC I  82 "
     model   vdw
     2.074 3.120
  nonbonded pdb=" OG  SER C  73 "
            pdb=" O   VAL C  78 "
     model   vdw
     2.085 3.040
  nonbonded pdb=" OG  SER G  73 "
            pdb=" O   VAL G  78 "
     model   vdw
     2.087 3.040
  nonbonded pdb=" N2   DG I 132 "
            pdb=" O2   DC J  16 "
     model   vdw
     2.099 2.496
  nonbonded pdb=" O   HIS F  75 "
            pdb=" NH1 ARG H  92 "
     model   vdw
     2.154 3.120
  ... (remaining 94841 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  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:             1.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     30.680
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
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      :  0.007   0.051  11186  Z= 0.325
  Angle     :  0.836  13.910  16173  Z= 0.502
  Chirality :  0.048   0.345   1850
  Planarity :  0.005   0.068   1178
  Dihedral  : 31.368 174.897   4788
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 25.84
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  6.61 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 12.06 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.81 (0.26), residues: 666
  helix: -1.35 (0.20), residues: 490
  sheet:  None (None), residues: 0
  loop : -2.95 (0.34), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS E 113 
 PHE   0.015   0.003   PHE F 100 
 TYR   0.015   0.002   TYR D  40 
 ARG   0.004   0.001   ARG C  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13718 (  698)
  hydrogen bonds       : angle       5.54592 ( 1753)
  covalent geometry    : bond        0.00701 (11186)
  covalent geometry    : angle       0.83576 (16173)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 214
  time to evaluate  : 0.757 
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   63 ARG cc_start: 0.7993 (mmp-170) cc_final: 0.7259 (mmp80)
REVERT: A   84 PHE cc_start: 0.8620 (m-80) cc_final: 0.8362 (m-80)
REVERT: A   90 MET cc_start: 0.8269 (mtp) cc_final: 0.7949 (mtp)
REVERT: A   93 GLN cc_start: 0.9115 (tt0) cc_final: 0.8566 (tt0)
REVERT: A   97 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8698 (mt-10)
REVERT: A  123 ASP cc_start: 0.8910 (m-30) cc_final: 0.8613 (m-30)
REVERT: B   27 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8814 (tm-30)
REVERT: B   63 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7692 (mt-10)
REVERT: B   88 TYR cc_start: 0.8335 (m-10) cc_final: 0.8043 (m-80)
REVERT: D   46 LYS cc_start: 0.8548 (mmtt) cc_final: 0.8174 (pttt)
REVERT: D   59 MET cc_start: 0.8768 (tpp) cc_final: 0.8280 (tpt)
REVERT: D   83 TYR cc_start: 0.7935 (m-10) cc_final: 0.7478 (m-10)
REVERT: D  105 GLU cc_start: 0.8753 (pp20) cc_final: 0.7935 (pm20)
REVERT: D  106 LEU cc_start: 0.8870 (mt) cc_final: 0.8608 (mt)
REVERT: E   60 LEU cc_start: 0.8172 (mt) cc_final: 0.7943 (mt)
REVERT: E   97 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8687 (mt-10)
REVERT: E  100 LEU cc_start: 0.9430 (tp) cc_final: 0.9150 (tt)
REVERT: F   88 TYR cc_start: 0.8285 (m-10) cc_final: 0.7234 (m-80)
REVERT: G   36 LEU cc_start: 0.9529 (tt) cc_final: 0.9310 (mm)
REVERT: G   46 VAL cc_start: 0.8463 (t) cc_final: 0.8236 (t)
REVERT: H   59 MET cc_start: 0.8789 (tpp) cc_final: 0.8525 (tpp)
REVERT: H  105 GLU cc_start: 0.8773 (pp20) cc_final: 0.8550 (pp20)
  outliers start: 4
  outliers final: 3
  residues processed: 218
  average time/residue: 0.3463
  time to fit residues: 96.3800
Evaluate side-chains
  144 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 141
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 68 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   chunk 23 optimal weight:    9.9990
   chunk 46 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 81 optimal weight:    6.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
C  71 ASN
H  95 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.048185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.037112 restraints weight = 85897.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.038248 restraints weight = 47845.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.038981 restraints weight = 32699.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.2911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  11186  Z= 0.185
  Angle     :  0.706   8.339  16173  Z= 0.412
  Chirality :  0.041   0.230   1850
  Planarity :  0.005   0.064   1178
  Dihedral  : 34.558 173.269   3476
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  2.25 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.31), residues: 666
  helix:  0.84 (0.22), residues: 506
  sheet:  None (None), residues: 0
  loop : -3.11 (0.34), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D  82 
 PHE   0.013   0.002   PHE E  67 
 TYR   0.013   0.002   TYR F  98 
 ARG   0.005   0.001   ARG C  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06187 (  698)
  hydrogen bonds       : angle       3.94397 ( 1753)
  covalent geometry    : bond        0.00396 (11186)
  covalent geometry    : angle       0.70638 (16173)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.727 
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: A   62 ILE cc_start: 0.9237 (mm) cc_final: 0.8969 (mm)
REVERT: A   63 ARG cc_start: 0.8536 (mmp-170) cc_final: 0.7882 (mmp80)
REVERT: A   84 PHE cc_start: 0.8860 (m-80) cc_final: 0.8472 (m-80)
REVERT: A   93 GLN cc_start: 0.9069 (tt0) cc_final: 0.8651 (tt0)
REVERT: A   97 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8684 (mt-10)
REVERT: A  126 LEU cc_start: 0.9501 (tp) cc_final: 0.9248 (tp)
REVERT: B   27 GLN cc_start: 0.9224 (mm-40) cc_final: 0.8885 (tm-30)
REVERT: B   49 LEU cc_start: 0.9174 (mp) cc_final: 0.8902 (mp)
REVERT: C   31 ARG cc_start: 0.8660 (ttm170) cc_final: 0.7933 (ttp80)
REVERT: D   62 MET cc_start: 0.9214 (tpp) cc_final: 0.8980 (tpp)
REVERT: D   71 GLU cc_start: 0.8536 (tp30) cc_final: 0.8324 (tp30)
REVERT: D   83 TYR cc_start: 0.7956 (m-10) cc_final: 0.7528 (m-80)
REVERT: D  102 LEU cc_start: 0.8479 (tp) cc_final: 0.8271 (tp)
REVERT: D  109 HIS cc_start: 0.8980 (m170) cc_final: 0.8710 (m90)
REVERT: E   93 GLN cc_start: 0.9240 (tt0) cc_final: 0.8697 (tp40)
REVERT: E   97 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8208 (mt-10)
REVERT: E  100 LEU cc_start: 0.9287 (tp) cc_final: 0.8996 (tp)
REVERT: F   27 GLN cc_start: 0.9243 (mm-40) cc_final: 0.8976 (mp10)
REVERT: F   58 LEU cc_start: 0.9238 (tt) cc_final: 0.9013 (pp)
REVERT: F   63 GLU cc_start: 0.8514 (mt-10) cc_final: 0.7969 (mt-10)
REVERT: G   31 ARG cc_start: 0.8667 (ttm170) cc_final: 0.8451 (ttp80)
REVERT: G   36 LEU cc_start: 0.9621 (tt) cc_final: 0.9380 (mm)
REVERT: H   79 ARG cc_start: 0.8450 (mtp180) cc_final: 0.8164 (mtp85)
REVERT: H   83 TYR cc_start: 0.7558 (m-10) cc_final: 0.7056 (m-80)
REVERT: H   95 GLN cc_start: 0.9258 (tt0) cc_final: 0.8984 (tt0)
REVERT: H  102 LEU cc_start: 0.8680 (tp) cc_final: 0.8410 (tp)
REVERT: H  109 HIS cc_start: 0.9122 (m170) cc_final: 0.8739 (m170)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.2908
  time to fit residues: 78.7116
Evaluate side-chains
  162 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 15 optimal weight:    8.9990
   chunk 89 optimal weight:   10.0000
   chunk 69 optimal weight:    7.9990
   chunk 51 optimal weight:    4.9990
   chunk 86 optimal weight:    6.9990
   chunk 78 optimal weight:   10.0000
   chunk 71 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 24 optimal weight:    0.7980
   chunk 77 optimal weight:   10.0000
   overall best weight:    4.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  43 HIS
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  33 HIS
G  43 HIS
H  63 ASN
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.045294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.033653 restraints weight = 90633.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.034728 restraints weight = 52463.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.035445 restraints weight = 36625.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.3585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048  11186  Z= 0.325
  Angle     :  0.785  11.476  16173  Z= 0.452
  Chirality :  0.043   0.182   1850
  Planarity :  0.006   0.058   1178
  Dihedral  : 34.573 172.091   3476
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 22.99
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  3.00 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.30), residues: 666
  helix:  0.94 (0.22), residues: 506
  sheet:  None (None), residues: 0
  loop : -3.09 (0.35), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS B  75 
 PHE   0.022   0.003   PHE B 100 
 TYR   0.019   0.003   TYR B  88 
 ARG   0.011   0.001   ARG G  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08249 (  698)
  hydrogen bonds       : angle       4.35989 ( 1753)
  covalent geometry    : bond        0.00706 (11186)
  covalent geometry    : angle       0.78520 (16173)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.9299 (mm) cc_final: 0.8891 (mm)
REVERT: A   63 ARG cc_start: 0.8587 (mmp-170) cc_final: 0.7891 (mmp80)
REVERT: A   70 LEU cc_start: 0.9627 (pp) cc_final: 0.9318 (tt)
REVERT: A   93 GLN cc_start: 0.9122 (tt0) cc_final: 0.8830 (tt0)
REVERT: A  100 LEU cc_start: 0.9328 (tp) cc_final: 0.9119 (tp)
REVERT: A  126 LEU cc_start: 0.9611 (tp) cc_final: 0.9377 (tp)
REVERT: A  128 ARG cc_start: 0.9215 (mtp-110) cc_final: 0.8958 (mmm-85)
REVERT: B   27 GLN cc_start: 0.9314 (mm-40) cc_final: 0.8901 (mp10)
REVERT: B   49 LEU cc_start: 0.9095 (mp) cc_final: 0.8889 (mp)
REVERT: C   31 ARG cc_start: 0.8516 (ttm170) cc_final: 0.8018 (ttp80)
REVERT: C   45 ARG cc_start: 0.8344 (mtp-110) cc_final: 0.8000 (mtp-110)
REVERT: C   57 ILE cc_start: 0.9253 (mm) cc_final: 0.9051 (mm)
REVERT: D   42 TYR cc_start: 0.9092 (m-80) cc_final: 0.8874 (m-80)
REVERT: D   80 LEU cc_start: 0.9703 (mt) cc_final: 0.9312 (mt)
REVERT: D   83 TYR cc_start: 0.7820 (m-10) cc_final: 0.7547 (m-80)
REVERT: D  102 LEU cc_start: 0.8351 (tp) cc_final: 0.8075 (tp)
REVERT: E   60 LEU cc_start: 0.8262 (mt) cc_final: 0.8047 (mt)
REVERT: E  100 LEU cc_start: 0.9460 (tp) cc_final: 0.9226 (tp)
REVERT: G   31 ARG cc_start: 0.8873 (ttm170) cc_final: 0.8447 (ttp-170)
REVERT: G   59 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8887 (mm-30)
REVERT: H   62 MET cc_start: 0.9406 (tmm) cc_final: 0.9086 (tmm)
REVERT: H   70 PHE cc_start: 0.9311 (t80) cc_final: 0.9109 (t80)
REVERT: H   80 LEU cc_start: 0.9651 (mt) cc_final: 0.9342 (mt)
REVERT: H   83 TYR cc_start: 0.7800 (m-10) cc_final: 0.7477 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.2613
  time to fit residues: 61.4645
Evaluate side-chains
  129 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 29 optimal weight:    8.9990
   chunk 37 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 70 optimal weight:    6.9990
   chunk 33 optimal weight:    8.9990
   chunk 77 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
E 113 HIS
H  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.048492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.036851 restraints weight = 82104.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.038027 restraints weight = 46388.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.038792 restraints weight = 32013.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.4458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11186  Z= 0.180
  Angle     :  0.681   7.868  16173  Z= 0.397
  Chirality :  0.040   0.247   1850
  Planarity :  0.005   0.060   1178
  Dihedral  : 34.267 174.133   3476
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 16.54
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  1.80 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.31), residues: 666
  helix:  1.48 (0.22), residues: 504
  sheet:  None (None), residues: 0
  loop : -3.05 (0.35), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS G  35 
 PHE   0.016   0.002   PHE E  84 
 TYR   0.028   0.002   TYR D  40 
 ARG   0.006   0.001   ARG H  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05907 (  698)
  hydrogen bonds       : angle       3.67752 ( 1753)
  covalent geometry    : bond        0.00390 (11186)
  covalent geometry    : angle       0.68111 (16173)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 1.025 
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: A   63 ARG cc_start: 0.8742 (mmp-170) cc_final: 0.8097 (mmp80)
REVERT: A   70 LEU cc_start: 0.9597 (pp) cc_final: 0.9376 (tt)
REVERT: A   93 GLN cc_start: 0.9172 (tt0) cc_final: 0.8913 (tp40)
REVERT: A  120 MET cc_start: 0.8923 (tpp) cc_final: 0.8692 (tpp)
REVERT: A  126 LEU cc_start: 0.9617 (tp) cc_final: 0.9360 (tp)
REVERT: B   27 GLN cc_start: 0.9353 (mm-40) cc_final: 0.8931 (mp10)
REVERT: B   63 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7977 (mt-10)
REVERT: B   84 MET cc_start: 0.8463 (tpp) cc_final: 0.8130 (tpp)
REVERT: C   57 ILE cc_start: 0.9224 (mm) cc_final: 0.9015 (mm)
REVERT: D  102 LEU cc_start: 0.8298 (tp) cc_final: 0.7917 (tp)
REVERT: D  109 HIS cc_start: 0.8888 (m90) cc_final: 0.8409 (m170)
REVERT: E   63 ARG cc_start: 0.8829 (mmp-170) cc_final: 0.8600 (mmp80)
REVERT: F   58 LEU cc_start: 0.9297 (tt) cc_final: 0.9082 (pp)
REVERT: F   63 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7917 (mt-10)
REVERT: G   31 ARG cc_start: 0.8679 (ttm170) cc_final: 0.7708 (ttp80)
REVERT: G   59 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8836 (mm-30)
REVERT: G   66 LEU cc_start: 0.9076 (mt) cc_final: 0.8729 (pp)
REVERT: H   42 TYR cc_start: 0.9130 (m-80) cc_final: 0.8901 (m-80)
REVERT: H   62 MET cc_start: 0.9427 (tmm) cc_final: 0.9205 (tmm)
REVERT: H  102 LEU cc_start: 0.8537 (tp) cc_final: 0.8233 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.2715
  time to fit residues: 66.2620
Evaluate side-chains
  144 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 56 optimal weight:    8.9990
   chunk 39 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 73 optimal weight:    8.9990
   chunk 80 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 63 optimal weight:    0.7980
   chunk 75 optimal weight:    6.9990
   chunk 76 optimal weight:    5.9990
   chunk 70 optimal weight:    8.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    2.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  35 HIS
H  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.047839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.035980 restraints weight = 84195.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.037120 restraints weight = 47968.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.037882 restraints weight = 33396.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.4882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11186  Z= 0.202
  Angle     :  0.674   7.850  16173  Z= 0.393
  Chirality :  0.039   0.229   1850
  Planarity :  0.005   0.061   1178
  Dihedral  : 34.177 171.962   3476
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 17.28
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  2.40 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.32), residues: 666
  helix:  1.42 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.91 (0.37), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C  35 
 PHE   0.017   0.002   PHE E 104 
 TYR   0.026   0.002   TYR F  72 
 ARG   0.008   0.001   ARG H  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06145 (  698)
  hydrogen bonds       : angle       3.74641 ( 1753)
  covalent geometry    : bond        0.00438 (11186)
  covalent geometry    : angle       0.67416 (16173)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.8715 (mmp-170) cc_final: 0.8135 (mmp80)
REVERT: A   93 GLN cc_start: 0.9167 (tt0) cc_final: 0.8809 (tt0)
REVERT: A  126 LEU cc_start: 0.9655 (tp) cc_final: 0.9405 (tp)
REVERT: B   27 GLN cc_start: 0.9317 (mm-40) cc_final: 0.8876 (mp10)
REVERT: B   63 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7997 (mt-10)
REVERT: D  102 LEU cc_start: 0.8319 (tp) cc_final: 0.7942 (tp)
REVERT: D  109 HIS cc_start: 0.8728 (m90) cc_final: 0.8526 (m90)
REVERT: E   93 GLN cc_start: 0.8712 (tp40) cc_final: 0.8431 (tp40)
REVERT: E  128 ARG cc_start: 0.9497 (mmm-85) cc_final: 0.9277 (mmm-85)
REVERT: F   27 GLN cc_start: 0.9290 (mm-40) cc_final: 0.8952 (mp10)
REVERT: F   49 LEU cc_start: 0.9088 (mp) cc_final: 0.8715 (mp)
REVERT: F   53 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8882 (mp0)
REVERT: F   58 LEU cc_start: 0.9285 (tt) cc_final: 0.9079 (pp)
REVERT: G   31 ARG cc_start: 0.8036 (ttm170) cc_final: 0.7313 (ttp-170)
REVERT: G   59 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8869 (mm-30)
REVERT: G   66 LEU cc_start: 0.9055 (mt) cc_final: 0.8734 (pp)
REVERT: H   62 MET cc_start: 0.9377 (tmm) cc_final: 0.9153 (tmm)
REVERT: H  102 LEU cc_start: 0.8497 (tp) cc_final: 0.8206 (tp)
REVERT: H  109 HIS cc_start: 0.8920 (m90) cc_final: 0.8404 (m170)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.2380
  time to fit residues: 57.7003
Evaluate side-chains
  132 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 68 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   chunk 52 optimal weight:    9.9990
   chunk 78 optimal weight:   10.0000
   chunk 42 optimal weight:    0.4980
   overall best weight:    2.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** 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 = 0.3328 r_free = 0.3328 target = 0.048209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.036430 restraints weight = 84686.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.037585 restraints weight = 48185.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.038353 restraints weight = 33521.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.5308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11186  Z= 0.196
  Angle     :  0.671   7.691  16173  Z= 0.389
  Chirality :  0.039   0.254   1850
  Planarity :  0.005   0.059   1178
  Dihedral  : 34.112 172.140   3476
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 17.28
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  2.40 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.32), residues: 666
  helix:  1.41 (0.22), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.72 (0.38), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E 113 
 PHE   0.011   0.001   PHE A 104 
 TYR   0.029   0.002   TYR H  40 
 ARG   0.006   0.001   ARG A 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06140 (  698)
  hydrogen bonds       : angle       3.69178 ( 1753)
  covalent geometry    : bond        0.00427 (11186)
  covalent geometry    : angle       0.67103 (16173)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.732 
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: A   62 ILE cc_start: 0.9272 (mm) cc_final: 0.9038 (mm)
REVERT: A   63 ARG cc_start: 0.8680 (mmp-170) cc_final: 0.8106 (mmp80)
REVERT: A   93 GLN cc_start: 0.9164 (tt0) cc_final: 0.8770 (tt0)
REVERT: A  123 ASP cc_start: 0.9132 (m-30) cc_final: 0.8883 (m-30)
REVERT: A  126 LEU cc_start: 0.9675 (tp) cc_final: 0.9451 (tp)
REVERT: B   27 GLN cc_start: 0.9353 (mm-40) cc_final: 0.8874 (mp10)
REVERT: B   63 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7966 (mt-10)
REVERT: B   88 TYR cc_start: 0.8602 (m-80) cc_final: 0.8365 (m-80)
REVERT: C   66 LEU cc_start: 0.9041 (mt) cc_final: 0.8560 (pp)
REVERT: D  102 LEU cc_start: 0.8304 (tp) cc_final: 0.7939 (tp)
REVERT: E   76 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8705 (tm-30)
REVERT: E   84 PHE cc_start: 0.9110 (m-80) cc_final: 0.8721 (m-80)
REVERT: E  123 ASP cc_start: 0.8583 (m-30) cc_final: 0.8381 (m-30)
REVERT: E  128 ARG cc_start: 0.9479 (mmm-85) cc_final: 0.9267 (mmm-85)
REVERT: F   27 GLN cc_start: 0.9292 (mm-40) cc_final: 0.8922 (mp10)
REVERT: F   58 LEU cc_start: 0.9255 (tt) cc_final: 0.9041 (pp)
REVERT: F   88 TYR cc_start: 0.8558 (m-10) cc_final: 0.7722 (m-80)
REVERT: G   35 HIS cc_start: 0.9021 (m90) cc_final: 0.8797 (m170)
REVERT: G   57 ILE cc_start: 0.9267 (mm) cc_final: 0.9040 (mm)
REVERT: G   59 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8769 (mm-30)
REVERT: G   66 LEU cc_start: 0.9056 (mt) cc_final: 0.8778 (pp)
REVERT: G  100 ILE cc_start: 0.8819 (mp) cc_final: 0.8609 (mp)
REVERT: H  102 LEU cc_start: 0.8521 (tp) cc_final: 0.8318 (tp)
REVERT: H  109 HIS cc_start: 0.8881 (m90) cc_final: 0.8509 (m170)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.2259
  time to fit residues: 53.5111
Evaluate side-chains
  131 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 54 optimal weight:   10.0000
   chunk 69 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9990
   chunk 86 optimal weight:    6.9990
   chunk 80 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9980
   chunk 74 optimal weight:    8.9990
   chunk 48 optimal weight:    7.9990
   chunk 79 optimal weight:   10.0000
   chunk 18 optimal weight:    3.9990
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
G  21 GLN
G  71 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.047356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.035640 restraints weight = 84818.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.036857 restraints weight = 46097.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.037670 restraints weight = 31183.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.5543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  11186  Z= 0.224
  Angle     :  0.691  11.213  16173  Z= 0.397
  Chirality :  0.040   0.247   1850
  Planarity :  0.005   0.057   1178
  Dihedral  : 34.159 171.640   3476
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 18.65
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  2.25 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.31), residues: 666
  helix:  1.32 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -2.67 (0.39), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 113 
 PHE   0.016   0.002   PHE H  70 
 TYR   0.031   0.002   TYR F  88 
 ARG   0.006   0.001   ARG A 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06705 (  698)
  hydrogen bonds       : angle       3.76402 ( 1753)
  covalent geometry    : bond        0.00490 (11186)
  covalent geometry    : angle       0.69120 (16173)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.9272 (mm) cc_final: 0.8899 (mm)
REVERT: A   63 ARG cc_start: 0.8688 (mmp-170) cc_final: 0.8098 (mmp80)
REVERT: A   93 GLN cc_start: 0.9163 (tt0) cc_final: 0.8732 (tt0)
REVERT: B   27 GLN cc_start: 0.9361 (mm-40) cc_final: 0.8854 (mp10)
REVERT: B   63 GLU cc_start: 0.8414 (mt-10) cc_final: 0.7996 (mt-10)
REVERT: C   31 ARG cc_start: 0.8462 (ttp-170) cc_final: 0.8119 (ttp-170)
REVERT: C   66 LEU cc_start: 0.9053 (mt) cc_final: 0.8578 (pp)
REVERT: D   80 LEU cc_start: 0.9681 (mt) cc_final: 0.9313 (mp)
REVERT: D  102 LEU cc_start: 0.8488 (tp) cc_final: 0.8105 (tp)
REVERT: E   84 PHE cc_start: 0.9110 (m-80) cc_final: 0.8802 (m-80)
REVERT: E   97 GLU cc_start: 0.9087 (pp20) cc_final: 0.8875 (pp20)
REVERT: F   27 GLN cc_start: 0.9313 (mm-40) cc_final: 0.8912 (mp10)
REVERT: F   49 LEU cc_start: 0.9222 (mp) cc_final: 0.8652 (mp)
REVERT: F   53 GLU cc_start: 0.9421 (mm-30) cc_final: 0.8911 (mp0)
REVERT: F   58 LEU cc_start: 0.9256 (tt) cc_final: 0.9031 (pp)
REVERT: F   63 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8177 (mt-10)
REVERT: G   35 HIS cc_start: 0.9012 (m90) cc_final: 0.8733 (m170)
REVERT: G   59 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8613 (mm-30)
REVERT: G   66 LEU cc_start: 0.9036 (mt) cc_final: 0.8724 (pp)
REVERT: G  100 ILE cc_start: 0.8759 (mp) cc_final: 0.8555 (mp)
REVERT: H  102 LEU cc_start: 0.8587 (tp) cc_final: 0.8364 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.2805
  time to fit residues: 63.3881
Evaluate side-chains
  122 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 71 optimal weight:    8.9990
   chunk 38 optimal weight:    8.9990
   chunk 51 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 89 optimal weight:   10.0000
   chunk 86 optimal weight:    6.9990
   chunk 87 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  21 GLN ** 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 = 0.3297 r_free = 0.3297 target = 0.047169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.035532 restraints weight = 83141.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.036741 restraints weight = 45492.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.037562 restraints weight = 30853.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.5779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  11186  Z= 0.233
  Angle     :  0.699   8.279  16173  Z= 0.404
  Chirality :  0.040   0.235   1850
  Planarity :  0.005   0.058   1178
  Dihedral  : 34.190 171.999   3476
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 19.71
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  2.40 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.31), residues: 666
  helix:  1.14 (0.22), residues: 510
  sheet:  None (None), residues: 0
  loop : -2.64 (0.40), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS A 113 
 PHE   0.014   0.002   PHE A 104 
 TYR   0.032   0.003   TYR F  88 
 ARG   0.006   0.001   ARG E 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06875 (  698)
  hydrogen bonds       : angle       3.85624 ( 1753)
  covalent geometry    : bond        0.00509 (11186)
  covalent geometry    : angle       0.69867 (16173)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.744 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.9286 (mm) cc_final: 0.8844 (mm)
REVERT: A   63 ARG cc_start: 0.8700 (mmp-170) cc_final: 0.8048 (mmp80)
REVERT: A   93 GLN cc_start: 0.9174 (tt0) cc_final: 0.8824 (tt0)
REVERT: B   27 GLN cc_start: 0.9327 (mm-40) cc_final: 0.8843 (mp10)
REVERT: B   46 ILE cc_start: 0.9063 (tp) cc_final: 0.8860 (pt)
REVERT: C   66 LEU cc_start: 0.9053 (mt) cc_final: 0.8578 (pp)
REVERT: D   80 LEU cc_start: 0.9711 (mt) cc_final: 0.9454 (mt)
REVERT: D   83 TYR cc_start: 0.7778 (m-80) cc_final: 0.7550 (m-80)
REVERT: D  102 LEU cc_start: 0.8468 (tp) cc_final: 0.8203 (tp)
REVERT: E   84 PHE cc_start: 0.9120 (m-80) cc_final: 0.8899 (m-80)
REVERT: E  120 MET cc_start: 0.8815 (tpp) cc_final: 0.8483 (tpp)
REVERT: F   27 GLN cc_start: 0.9300 (mm-40) cc_final: 0.8901 (mp10)
REVERT: F   49 LEU cc_start: 0.9107 (mp) cc_final: 0.8566 (mp)
REVERT: F   53 GLU cc_start: 0.9451 (mm-30) cc_final: 0.8899 (mp0)
REVERT: G   66 LEU cc_start: 0.9030 (mt) cc_final: 0.8721 (pp)
REVERT: H  102 LEU cc_start: 0.8606 (tp) cc_final: 0.8269 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.2161
  time to fit residues: 49.5275
Evaluate side-chains
  122 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 50 optimal weight:    6.9990
   chunk 70 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9990
   chunk 86 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   chunk 73 optimal weight:    7.9990
   chunk 44 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 83 optimal weight:    6.9990
   chunk 75 optimal weight:    6.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  21 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.048036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.036811 restraints weight = 86525.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.037950 restraints weight = 47965.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.038690 restraints weight = 32994.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.6064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  11186  Z= 0.186
  Angle     :  0.675   8.503  16173  Z= 0.387
  Chirality :  0.039   0.255   1850
  Planarity :  0.005   0.062   1178
  Dihedral  : 34.075 172.386   3476
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 17.60
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  2.25 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.60 %
    Favored  : 98.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.32), residues: 666
  helix:  1.32 (0.23), residues: 510
  sheet:  None (None), residues: 0
  loop : -2.47 (0.41), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 113 
 PHE   0.022   0.002   PHE E 104 
 TYR   0.021   0.002   TYR H  83 
 ARG   0.007   0.001   ARG A 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06096 (  698)
  hydrogen bonds       : angle       3.65765 ( 1753)
  covalent geometry    : bond        0.00406 (11186)
  covalent geometry    : angle       0.67504 (16173)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 166
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.8664 (mmp-170) cc_final: 0.8072 (mmp80)
REVERT: A   93 GLN cc_start: 0.9166 (tt0) cc_final: 0.8872 (tp40)
REVERT: A  123 ASP cc_start: 0.8942 (m-30) cc_final: 0.8730 (m-30)
REVERT: A  128 ARG cc_start: 0.9302 (mmm-85) cc_final: 0.9046 (mmm-85)
REVERT: B   27 GLN cc_start: 0.9272 (mm-40) cc_final: 0.8842 (mp10)
REVERT: B   53 GLU cc_start: 0.7733 (mp0) cc_final: 0.7511 (mp0)
REVERT: B   63 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8067 (mt-10)
REVERT: C   31 ARG cc_start: 0.8371 (ttp-170) cc_final: 0.7622 (ttp-170)
REVERT: C   66 LEU cc_start: 0.8951 (mt) cc_final: 0.8545 (pp)
REVERT: D   83 TYR cc_start: 0.8068 (m-80) cc_final: 0.7330 (m-80)
REVERT: D  102 LEU cc_start: 0.8352 (tp) cc_final: 0.8125 (tp)
REVERT: E   84 PHE cc_start: 0.9105 (m-80) cc_final: 0.8835 (m-80)
REVERT: E  120 MET cc_start: 0.8785 (tpp) cc_final: 0.8568 (tpp)
REVERT: F   27 GLN cc_start: 0.9244 (mm-40) cc_final: 0.8849 (mp10)
REVERT: F   63 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8122 (mt-10)
REVERT: G   31 ARG cc_start: 0.8535 (ttp-170) cc_final: 0.8251 (ttp-170)
REVERT: G   66 LEU cc_start: 0.8988 (mt) cc_final: 0.8685 (pp)
REVERT: G  100 ILE cc_start: 0.8760 (mp) cc_final: 0.8535 (mp)
REVERT: H  102 LEU cc_start: 0.8585 (tp) cc_final: 0.8205 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 167
  average time/residue: 0.2262
  time to fit residues: 52.4108
Evaluate side-chains
  122 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 69 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9980
   chunk 17 optimal weight:    0.4980
   chunk 9 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 57 optimal weight:    4.9990
   chunk 78 optimal weight:   10.0000
   chunk 29 optimal weight:    9.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
D  63 ASN
** G  21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.049970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.038472 restraints weight = 84697.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.039636 restraints weight = 47811.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.040440 restraints weight = 33009.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.6592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11186  Z= 0.163
  Angle     :  0.670   8.900  16173  Z= 0.382
  Chirality :  0.039   0.282   1850
  Planarity :  0.005   0.064   1178
  Dihedral  : 33.839 172.075   3476
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 15.48
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  2.25 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.32), residues: 666
  helix:  1.27 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.27 (0.42), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.001   HIS G  35 
 PHE   0.014   0.001   PHE E 104 
 TYR   0.029   0.002   TYR F  88 
 ARG   0.012   0.001   ARG A 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05497 (  698)
  hydrogen bonds       : angle       3.54332 ( 1753)
  covalent geometry    : bond        0.00350 (11186)
  covalent geometry    : angle       0.66992 (16173)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.8648 (mmp-170) cc_final: 0.8051 (mmp80)
REVERT: B   27 GLN cc_start: 0.9189 (mm-40) cc_final: 0.8794 (mp10)
REVERT: B   63 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8065 (mt-10)
REVERT: C   66 LEU cc_start: 0.8955 (mt) cc_final: 0.8584 (pp)
REVERT: D   80 LEU cc_start: 0.9474 (mp) cc_final: 0.9262 (mt)
REVERT: D   83 TYR cc_start: 0.7610 (m-80) cc_final: 0.7185 (m-80)
REVERT: D  102 LEU cc_start: 0.8194 (tp) cc_final: 0.7930 (tp)
REVERT: E   84 PHE cc_start: 0.8937 (m-80) cc_final: 0.8646 (m-80)
REVERT: F   27 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8814 (mp10)
REVERT: F   49 LEU cc_start: 0.9135 (mp) cc_final: 0.8037 (mp)
REVERT: F   53 GLU cc_start: 0.9358 (mm-30) cc_final: 0.9037 (mp0)
REVERT: F   63 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7962 (mt-10)
REVERT: G   31 ARG cc_start: 0.8305 (ttp-170) cc_final: 0.7717 (ttp-170)
REVERT: G   66 LEU cc_start: 0.8964 (mt) cc_final: 0.8698 (pp)
REVERT: G  100 ILE cc_start: 0.8571 (mp) cc_final: 0.8353 (mp)
REVERT: H  102 LEU cc_start: 0.8495 (tp) cc_final: 0.8138 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.2170
  time to fit residues: 52.3890
Evaluate side-chains
  134 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 70 optimal weight:    8.9990
   chunk 40 optimal weight:    7.9990
   chunk 21 optimal weight:    5.9990
   chunk 17 optimal weight:    9.9990
   chunk 56 optimal weight:    0.9990
   chunk 79 optimal weight:    9.9990
   chunk 36 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 53 optimal weight:   10.0000
   chunk 74 optimal weight:    8.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  63 ASN
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  35 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.047599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.036041 restraints weight = 87538.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.037120 restraints weight = 51272.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.037863 restraints weight = 36173.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.6534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  11186  Z= 0.231
  Angle     :  0.706   8.751  16173  Z= 0.404
  Chirality :  0.040   0.265   1850
  Planarity :  0.005   0.060   1178
  Dihedral  : 33.988 171.364   3476
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 20.50
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  2.10 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.31), residues: 666
  helix:  1.16 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -2.30 (0.43), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.002   HIS G  35 
 PHE   0.021   0.002   PHE E 104 
 TYR   0.024   0.002   TYR F  88 
 ARG   0.012   0.001   ARG A 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06769 (  698)
  hydrogen bonds       : angle       3.74838 ( 1753)
  covalent geometry    : bond        0.00506 (11186)
  covalent geometry    : angle       0.70643 (16173)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3070.94 seconds
wall clock time: 55 minutes 21.36 seconds (3321.36 seconds total)