Starting phenix.real_space_refine
on Wed Mar  4 02:46:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6m4d_30076/03_2026/6m4d_30076.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6m4d_30076/03_2026/6m4d_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_30076/03_2026/6m4d_30076.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6m4d_30076/03_2026/6m4d_30076.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6m4d_30076/03_2026/6m4d_30076.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6m4d_30076/03_2026/6m4d_30076.cif"
  }
  resolution = 4.4
  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=   0.001 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): 0.00s

  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: 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: 2.12, per 1000 atoms: 0.20
  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: 0.68
  Conformation dependent library (CDL) restraints added in 249.2 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: 1.67
  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: 1.81

  Time building geometry restraints manager: 0.91 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:             1.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.740
  Find NCS groups from input model:        0.090
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.740
-------------------------------------------------------------------------------
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 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: -2.81 (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
 ARG   0.004   0.001   ARG C  31 
 TYR   0.015   0.002   TYR D  40 
 PHE   0.015   0.003   PHE F 100 
 HIS   0.006   0.002   HIS E 113 

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

*********************** 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  : 0.267 
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: 0.9116 (tt0) cc_final: 0.8566 (tt0)
REVERT: A   97 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8699 (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: 0.8813 (tm-30)
REVERT: B   63 GLU cc_start: 0.8266 (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: 0.7479 (m-10)
REVERT: D  105 GLU cc_start: 0.8752 (pp20) cc_final: 0.7934 (pm20)
REVERT: D  106 LEU cc_start: 0.8870 (mt) cc_final: 0.8608 (mt)
REVERT: E   60 LEU cc_start: 0.8171 (mt) cc_final: 0.7942 (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: 0.7235 (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: 0.1401
  time to fit residues: 39.2309
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  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    8.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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
C  71 ASN
G  43 HIS
H  95 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.047039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.035226 restraints weight = 87343.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.036308 restraints weight = 50672.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.037039 restraints weight = 35704.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.037508 restraints weight = 28442.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.037699 restraints weight = 24681.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.2642

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     :  0.736  10.702  16173  Z= 0.428
  Chirality :  0.042   0.209   1850
  Planarity :  0.005   0.064   1178
  Dihedral  : 34.701 172.731   3476
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 17.60
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  2.40 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  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: -0.40 (0.30), residues: 666
  helix:  0.61 (0.22), residues: 506
  sheet:  None (None), residues: 0
  loop : -3.07 (0.35), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 131 
 TYR   0.011   0.002   TYR F  98 
 PHE   0.014   0.002   PHE E 104 
 HIS   0.007   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 (11186)
  covalent geometry    : angle       0.73562 (16173)
  hydrogen bonds       : bond        0.06990 (  698)
  hydrogen bonds       : angle       4.19386 ( 1753)

*********************** 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
  191 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.9266 (mm) cc_final: 0.8930 (mm)
REVERT: A   63 ARG cc_start: 0.8591 (mmp-170) cc_final: 0.7910 (mmp80)
REVERT: A   84 PHE cc_start: 0.8885 (m-80) cc_final: 0.8630 (m-80)
REVERT: A   90 MET cc_start: 0.8450 (mtp) cc_final: 0.8217 (mtp)
REVERT: A   93 GLN cc_start: 0.9094 (tt0) cc_final: 0.8657 (tt0)
REVERT: A   97 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8788 (mt-10)
REVERT: A  126 LEU cc_start: 0.9539 (tp) cc_final: 0.9275 (tp)
REVERT: B   27 GLN cc_start: 0.9278 (mm-40) cc_final: 0.8928 (tm-30)
REVERT: B   63 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7915 (mt-10)
REVERT: B   96 THR cc_start: 0.8390 (t) cc_final: 0.7861 (m)
REVERT: C   31 ARG cc_start: 0.8764 (ttm170) cc_final: 0.8126 (ttp80)
REVERT: D   62 MET cc_start: 0.9292 (tpp) cc_final: 0.8997 (tpp)
REVERT: D   83 TYR cc_start: 0.7819 (m-10) cc_final: 0.7306 (m-80)
REVERT: D  102 LEU cc_start: 0.8481 (tp) cc_final: 0.8139 (tp)
REVERT: D  109 HIS cc_start: 0.9085 (m170) cc_final: 0.8663 (m170)
REVERT: E  100 LEU cc_start: 0.9397 (tp) cc_final: 0.9134 (tp)
REVERT: F   58 LEU cc_start: 0.9266 (tt) cc_final: 0.9021 (pp)
REVERT: F   63 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7996 (mt-10)
REVERT: F   84 MET cc_start: 0.8311 (tpt) cc_final: 0.8080 (tpp)
REVERT: G   31 ARG cc_start: 0.8823 (ttm170) cc_final: 0.7957 (ttp80)
REVERT: G   36 LEU cc_start: 0.9659 (tt) cc_final: 0.9415 (mm)
REVERT: G   45 ARG cc_start: 0.8086 (mtp-110) cc_final: 0.7816 (mtp-110)
REVERT: H   79 ARG cc_start: 0.8634 (mtp180) cc_final: 0.8225 (mtp85)
REVERT: H   83 TYR cc_start: 0.7592 (m-10) cc_final: 0.7123 (m-10)
REVERT: H   95 GLN cc_start: 0.9242 (tt0) cc_final: 0.8975 (tt0)
REVERT: H  102 LEU cc_start: 0.8745 (tp) cc_final: 0.8447 (tp)
REVERT: H  109 HIS cc_start: 0.9158 (m170) cc_final: 0.8738 (m170)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.1207
  time to fit residues: 30.5389
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  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   chunk 15 optimal weight:    9.9990
   chunk 87 optimal weight:    6.9990
   chunk 50 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 78 optimal weight:   10.0000
   chunk 69 optimal weight:    5.9990
   overall best weight:    3.5588

-------------------------------------------------------------------------------
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**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 113 HIS
H  63 ASN
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.046069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.034497 restraints weight = 87273.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.035562 restraints weight = 50571.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.036266 restraints weight = 35435.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.036700 restraints weight = 28172.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.037034 restraints weight = 24468.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.3522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  11186  Z= 0.267
  Angle     :  0.733  10.828  16173  Z= 0.425
  Chirality :  0.041   0.185   1850
  Planarity :  0.005   0.057   1178
  Dihedral  : 34.518 172.379   3476
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 19.76
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  2.55 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.25 (0.31), residues: 666
  helix:  1.12 (0.22), residues: 506
  sheet:  None (None), residues: 0
  loop : -3.00 (0.35), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G  31 
 TYR   0.019   0.002   TYR B  88 
 PHE   0.014   0.002   PHE F 100 
 HIS   0.007   0.002   HIS H 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00579 (11186)
  covalent geometry    : angle       0.73341 (16173)
  hydrogen bonds       : bond        0.07326 (  698)
  hydrogen bonds       : angle       4.09782 ( 1753)

*********************** 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
  176 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.205 
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: 0.9280 (mm) cc_final: 0.9071 (mm)
REVERT: A   63 ARG cc_start: 0.8614 (mmp-170) cc_final: 0.7999 (mmp80)
REVERT: A   70 LEU cc_start: 0.9677 (pp) cc_final: 0.9399 (tt)
REVERT: A   90 MET cc_start: 0.8550 (mtp) cc_final: 0.8335 (mtp)
REVERT: A   93 GLN cc_start: 0.8982 (tt0) cc_final: 0.8655 (tp40)
REVERT: A   97 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8484 (mt-10)
REVERT: B   27 GLN cc_start: 0.9279 (mm-40) cc_final: 0.8789 (tm-30)
REVERT: C   31 ARG cc_start: 0.8653 (ttm170) cc_final: 0.8134 (ttp80)
REVERT: C   57 ILE cc_start: 0.9218 (mm) cc_final: 0.9015 (mm)
REVERT: D   42 TYR cc_start: 0.9125 (m-80) cc_final: 0.8822 (m-80)
REVERT: D   62 MET cc_start: 0.9256 (tpp) cc_final: 0.9055 (tpp)
REVERT: D   72 ARG cc_start: 0.9254 (mtt180) cc_final: 0.8890 (mmm-85)
REVERT: D   80 LEU cc_start: 0.9672 (mt) cc_final: 0.9356 (mt)
REVERT: D   83 TYR cc_start: 0.7815 (m-10) cc_final: 0.7480 (m-80)
REVERT: D  102 LEU cc_start: 0.8414 (tp) cc_final: 0.8150 (tp)
REVERT: E   60 LEU cc_start: 0.8245 (mt) cc_final: 0.8022 (mt)
REVERT: E   63 ARG cc_start: 0.8889 (mmp-170) cc_final: 0.8554 (mmp80)
REVERT: E  100 LEU cc_start: 0.9409 (tp) cc_final: 0.9166 (tp)
REVERT: E  105 GLU cc_start: 0.9203 (tp30) cc_final: 0.8993 (tp30)
REVERT: F   84 MET cc_start: 0.8480 (tpt) cc_final: 0.8039 (tpp)
REVERT: G   31 ARG cc_start: 0.8543 (ttm170) cc_final: 0.8069 (ttp80)
REVERT: G   37 LYS cc_start: 0.9180 (mmmt) cc_final: 0.8944 (mmtm)
REVERT: H   70 PHE cc_start: 0.9304 (t80) cc_final: 0.9099 (t80)
REVERT: H   80 LEU cc_start: 0.9651 (mt) cc_final: 0.9326 (mt)
REVERT: H   83 TYR cc_start: 0.7698 (m-10) cc_final: 0.7360 (m-80)
REVERT: H   95 GLN cc_start: 0.9158 (tt0) cc_final: 0.8956 (tt0)
REVERT: H  105 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8519 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.1110
  time to fit residues: 26.1427
Evaluate side-chains
  130 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0770
   chunk 35 optimal weight:    4.9990
   chunk 62 optimal weight:   10.0000
   chunk 30 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   chunk 23 optimal weight:    8.9990
   chunk 14 optimal weight:    7.9990
   chunk 55 optimal weight:    9.9990
   chunk 60 optimal weight:    4.9990
   chunk 84 optimal weight:    5.9990
   overall best weight:    2.6144

-------------------------------------------------------------------------------
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**
A 113 HIS
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
G  35 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 = 0.3293 r_free = 0.3293 target = 0.047064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.035656 restraints weight = 82202.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.036859 restraints weight = 44475.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.037668 restraints weight = 29783.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.038166 restraints weight = 22950.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.038498 restraints weight = 19544.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.4247

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= 0.222
  Angle     :  0.698   8.089  16173  Z= 0.406
  Chirality :  0.040   0.229   1850
  Planarity :  0.005   0.062   1178
  Dihedral  : 34.354 173.157   3476
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 18.34
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  2.40 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  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:  0.51 (0.31), residues: 666
  helix:  1.31 (0.22), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.87 (0.37), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  86 
 TYR   0.034   0.003   TYR H  40 
 PHE   0.016   0.002   PHE A 104 
 HIS   0.005   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 (11186)
  covalent geometry    : angle       0.69769 (16173)
  hydrogen bonds       : bond        0.06449 (  698)
  hydrogen bonds       : angle       3.85549 ( 1753)

*********************** 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
  178 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.210 
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: 0.8660 (mmp-170) cc_final: 0.8054 (mmp80)
REVERT: A   70 LEU cc_start: 0.9688 (pp) cc_final: 0.9445 (tt)
REVERT: A   93 GLN cc_start: 0.8992 (tt0) cc_final: 0.8536 (tp40)
REVERT: A   97 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8540 (mt-10)
REVERT: B   27 GLN cc_start: 0.9334 (mm-40) cc_final: 0.8894 (mp10)
REVERT: B   84 MET cc_start: 0.8544 (tpp) cc_final: 0.8341 (tpp)
REVERT: C   31 ARG cc_start: 0.8671 (ttm170) cc_final: 0.8418 (ttp80)
REVERT: C   57 ILE cc_start: 0.9218 (mm) cc_final: 0.9011 (mm)
REVERT: D   62 MET cc_start: 0.9289 (tpp) cc_final: 0.9071 (tpp)
REVERT: D  102 LEU cc_start: 0.8383 (tp) cc_final: 0.8041 (tp)
REVERT: E   63 ARG cc_start: 0.8885 (mmp-170) cc_final: 0.8573 (mmp80)
REVERT: E  105 GLU cc_start: 0.9244 (tp30) cc_final: 0.9024 (tp30)
REVERT: F   27 GLN cc_start: 0.9304 (mm-40) cc_final: 0.9018 (mp10)
REVERT: F   58 LEU cc_start: 0.9290 (tt) cc_final: 0.9048 (pp)
REVERT: G   31 ARG cc_start: 0.8475 (ttm170) cc_final: 0.7882 (ttp80)
REVERT: H   42 TYR cc_start: 0.9103 (m-80) cc_final: 0.8885 (m-80)
REVERT: H  109 HIS cc_start: 0.9046 (m170) cc_final: 0.8809 (m170)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.1124
  time to fit residues: 26.6289
Evaluate side-chains
  139 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 87 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9980
   chunk 68 optimal weight:    7.9990
   chunk 89 optimal weight:   10.0000
   chunk 58 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   overall best weight:    1.7384

-------------------------------------------------------------------------------
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  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  33 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 = 0.3326 r_free = 0.3326 target = 0.048132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.036186 restraints weight = 83268.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.037355 restraints weight = 46037.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.038151 restraints weight = 31662.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.038640 restraints weight = 24888.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.038971 restraints weight = 21459.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.4813

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= 0.187
  Angle     :  0.666   7.946  16173  Z= 0.388
  Chirality :  0.039   0.248   1850
  Planarity :  0.005   0.059   1178
  Dihedral  : 34.162 172.849   3476
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 16.75
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  1.95 %
    Favored  : 97.45 %
  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 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:  0.81 (0.32), residues: 666
  helix:  1.51 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.68 (0.39), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 128 
 TYR   0.028   0.002   TYR H  40 
 PHE   0.015   0.002   PHE H  70 
 HIS   0.004   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 (11186)
  covalent geometry    : angle       0.66601 (16173)
  hydrogen bonds       : bond        0.06015 (  698)
  hydrogen bonds       : angle       3.66011 ( 1753)

*********************** 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
  185 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.9255 (mm) cc_final: 0.9014 (mm)
REVERT: A   63 ARG cc_start: 0.8685 (mmp-170) cc_final: 0.8109 (mmp80)
REVERT: A   70 LEU cc_start: 0.9690 (pp) cc_final: 0.9469 (tt)
REVERT: A   93 GLN cc_start: 0.9010 (tt0) cc_final: 0.8670 (tt0)
REVERT: A  126 LEU cc_start: 0.9573 (tp) cc_final: 0.9307 (tp)
REVERT: A  133 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6997 (mt-10)
REVERT: B   27 GLN cc_start: 0.9318 (mm-40) cc_final: 0.8896 (mp10)
REVERT: B   63 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7971 (mt-10)
REVERT: B   74 GLU cc_start: 0.8903 (tp30) cc_final: 0.8610 (tp30)
REVERT: B   84 MET cc_start: 0.8543 (tpp) cc_final: 0.8205 (tpp)
REVERT: D   62 MET cc_start: 0.9302 (tpp) cc_final: 0.9054 (tpp)
REVERT: D  102 LEU cc_start: 0.8381 (tp) cc_final: 0.8032 (tp)
REVERT: D  109 HIS cc_start: 0.9156 (m170) cc_final: 0.8507 (m170)
REVERT: E   76 GLN cc_start: 0.8899 (tp40) cc_final: 0.8688 (tp40)
REVERT: E   97 GLU cc_start: 0.9015 (pp20) cc_final: 0.8790 (pp20)
REVERT: E  128 ARG cc_start: 0.9428 (mmm-85) cc_final: 0.9219 (mmm-85)
REVERT: F   27 GLN cc_start: 0.9255 (mm-40) cc_final: 0.8954 (mp10)
REVERT: F   58 LEU cc_start: 0.9272 (tt) cc_final: 0.9031 (pp)
REVERT: G   31 ARG cc_start: 0.8638 (ttm170) cc_final: 0.7797 (ttp80)
REVERT: G   45 ARG cc_start: 0.8100 (mtp-110) cc_final: 0.7833 (mtp-110)
REVERT: G   66 LEU cc_start: 0.9041 (mt) cc_final: 0.8723 (pp)
REVERT: H  102 LEU cc_start: 0.8372 (tp) cc_final: 0.8018 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.1074
  time to fit residues: 26.9797
Evaluate side-chains
  133 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 65 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 69 optimal weight:    6.9990
   chunk 72 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 83 optimal weight:    7.9990
   chunk 4 optimal weight:    3.9990
   chunk 82 optimal weight:    7.9990
   chunk 51 optimal weight:    7.9990
   overall best weight:    3.5788

-------------------------------------------------------------------------------
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  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 109 HIS
** 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 = 0.3282 r_free = 0.3282 target = 0.046478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.034736 restraints weight = 86822.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.035867 restraints weight = 48978.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.036605 restraints weight = 33859.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.037101 restraints weight = 26865.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.037340 restraints weight = 23115.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.5096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  11186  Z= 0.266
  Angle     :  0.730  13.437  16173  Z= 0.420
  Chirality :  0.041   0.230   1850
  Planarity :  0.006   0.055   1178
  Dihedral  : 34.274 172.002   3476
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 20.87
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  3.00 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.43 (0.31), residues: 666
  helix:  1.19 (0.22), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.66 (0.39), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  39 
 TYR   0.031   0.002   TYR H  40 
 PHE   0.020   0.002   PHE A 104 
 HIS   0.008   0.002   HIS D 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00579 (11186)
  covalent geometry    : angle       0.72968 (16173)
  hydrogen bonds       : bond        0.07413 (  698)
  hydrogen bonds       : angle       3.95373 ( 1753)

*********************** 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
  160 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.226 
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: 0.9340 (mm) cc_final: 0.9094 (mm)
REVERT: A   63 ARG cc_start: 0.8640 (mmp-170) cc_final: 0.7966 (mmp80)
REVERT: A   70 LEU cc_start: 0.9681 (pp) cc_final: 0.9430 (tt)
REVERT: A   93 GLN cc_start: 0.9019 (tt0) cc_final: 0.8425 (tp40)
REVERT: A   97 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8211 (mt-10)
REVERT: A  100 LEU cc_start: 0.9241 (tp) cc_final: 0.9011 (tp)
REVERT: B   27 GLN cc_start: 0.9303 (mm-40) cc_final: 0.8857 (mp10)
REVERT: C   35 HIS cc_start: 0.9125 (m90) cc_final: 0.8742 (m-70)
REVERT: D   37 TYR cc_start: 0.9111 (m-80) cc_final: 0.8842 (m-80)
REVERT: D  102 LEU cc_start: 0.8347 (tp) cc_final: 0.8020 (tp)
REVERT: F   27 GLN cc_start: 0.9254 (mm-40) cc_final: 0.8921 (mp10)
REVERT: F   58 LEU cc_start: 0.9276 (tt) cc_final: 0.9003 (pp)
REVERT: G   59 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8529 (mm-30)
REVERT: G   66 LEU cc_start: 0.8993 (mt) cc_final: 0.8692 (pp)
REVERT: H   35 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7357 (mm-30)
REVERT: H  102 LEU cc_start: 0.8483 (tp) cc_final: 0.8152 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.0980
  time to fit residues: 21.8322
Evaluate side-chains
  117 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 33 optimal weight:    8.9990
   chunk 80 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9990
   chunk 66 optimal weight:   10.0000
   chunk 42 optimal weight:    1.9990
   chunk 79 optimal weight:    8.9990
   chunk 77 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.7990

-------------------------------------------------------------------------------
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 = 0.3322 r_free = 0.3322 target = 0.048035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.036602 restraints weight = 82240.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.037794 restraints weight = 44327.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.038602 restraints weight = 29958.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.039108 restraints weight = 23229.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.039470 restraints weight = 19837.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.5487

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= 0.188
  Angle     :  0.676   8.249  16173  Z= 0.389
  Chirality :  0.039   0.252   1850
  Planarity :  0.005   0.058   1178
  Dihedral  : 34.211 173.044   3476
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 17.28
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  1.95 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.42 %
    Favored  : 98.40 %
  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:  0.57 (0.31), residues: 666
  helix:  1.29 (0.22), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.60 (0.40), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 128 
 TYR   0.024   0.002   TYR H  40 
 PHE   0.016   0.002   PHE H  70 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (11186)
  covalent geometry    : angle       0.67579 (16173)
  hydrogen bonds       : bond        0.06148 (  698)
  hydrogen bonds       : angle       3.68924 ( 1753)

*********************** 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
  179 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 178
  time to evaluate  : 0.195 
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: 0.9293 (mm) cc_final: 0.8774 (mm)
REVERT: A   63 ARG cc_start: 0.8627 (mmp-170) cc_final: 0.8004 (mmp80)
REVERT: A   70 LEU cc_start: 0.9673 (pp) cc_final: 0.9461 (tt)
REVERT: A   93 GLN cc_start: 0.9038 (tt0) cc_final: 0.8488 (tt0)
REVERT: A   94 GLU cc_start: 0.9058 (tt0) cc_final: 0.8497 (tt0)
REVERT: B   27 GLN cc_start: 0.9260 (mm-40) cc_final: 0.8839 (mp10)
REVERT: B   63 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7980 (mt-10)
REVERT: B   88 TYR cc_start: 0.8613 (m-80) cc_final: 0.8392 (m-80)
REVERT: C   35 HIS cc_start: 0.9235 (m90) cc_final: 0.8850 (m-70)
REVERT: C   45 ARG cc_start: 0.8319 (mtm-85) cc_final: 0.7815 (mtm-85)
REVERT: C   66 LEU cc_start: 0.9057 (mt) cc_final: 0.8594 (pp)
REVERT: D   37 TYR cc_start: 0.9150 (m-80) cc_final: 0.8872 (m-80)
REVERT: D  102 LEU cc_start: 0.8253 (tp) cc_final: 0.7947 (tp)
REVERT: E   90 MET cc_start: 0.8490 (mtt) cc_final: 0.8131 (mtt)
REVERT: E   97 GLU cc_start: 0.9153 (pp20) cc_final: 0.8834 (pp20)
REVERT: E  128 ARG cc_start: 0.9454 (mmm-85) cc_final: 0.9250 (mmm-85)
REVERT: F   27 GLN cc_start: 0.9312 (mm-40) cc_final: 0.8929 (mp10)
REVERT: F   58 LEU cc_start: 0.9236 (tt) cc_final: 0.8985 (pp)
REVERT: G   31 ARG cc_start: 0.8628 (ttm170) cc_final: 0.8050 (ttp80)
REVERT: G   35 HIS cc_start: 0.9071 (m90) cc_final: 0.8568 (m170)
REVERT: G   57 ILE cc_start: 0.9283 (mm) cc_final: 0.9029 (mm)
REVERT: G   66 LEU cc_start: 0.8940 (mt) cc_final: 0.8661 (pp)
REVERT: H  102 LEU cc_start: 0.8508 (tp) cc_final: 0.8157 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 179
  average time/residue: 0.0998
  time to fit residues: 24.7162
Evaluate side-chains
  128 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 59 optimal weight:    0.3980
   chunk 18 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 31 optimal weight:    8.9990
   chunk 80 optimal weight:    8.9990
   chunk 66 optimal weight:    9.9990
   chunk 58 optimal weight:    3.9990
   chunk 62 optimal weight:    6.9990
   chunk 11 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3363 r_free = 0.3363 target = 0.049799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.038194 restraints weight = 85357.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.039328 restraints weight = 49204.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.040075 restraints weight = 34449.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.040565 restraints weight = 27394.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.040815 restraints weight = 23705.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.6068

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= 0.160
  Angle     :  0.656   8.828  16173  Z= 0.373
  Chirality :  0.038   0.255   1850
  Planarity :  0.005   0.061   1178
  Dihedral  : 33.971 171.743   3476
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 14.96
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.45 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  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:  0.82 (0.32), residues: 666
  helix:  1.46 (0.23), residues: 502
  sheet:  None (None), residues: 0
  loop : -2.44 (0.41), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  92 
 TYR   0.018   0.001   TYR H  40 
 PHE   0.017   0.002   PHE E 104 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (11186)
  covalent geometry    : angle       0.65573 (16173)
  hydrogen bonds       : bond        0.05520 (  698)
  hydrogen bonds       : angle       3.42911 ( 1753)

*********************** 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
  184 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.8636 (mmp-170) cc_final: 0.8076 (mmp80)
REVERT: A   70 LEU cc_start: 0.9670 (pp) cc_final: 0.9357 (tt)
REVERT: B   27 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8750 (mp10)
REVERT: B   63 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7987 (mt-10)
REVERT: B   88 TYR cc_start: 0.8480 (m-80) cc_final: 0.8273 (m-80)
REVERT: C   31 ARG cc_start: 0.8561 (ptt180) cc_final: 0.7726 (ptt180)
REVERT: C   35 HIS cc_start: 0.9130 (m90) cc_final: 0.8722 (m-70)
REVERT: C   45 ARG cc_start: 0.8180 (mtm-85) cc_final: 0.7474 (mtt180)
REVERT: C   66 LEU cc_start: 0.9056 (mt) cc_final: 0.8584 (pp)
REVERT: D  102 LEU cc_start: 0.8181 (tp) cc_final: 0.7692 (tp)
REVERT: D  105 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8397 (tm-30)
REVERT: E  120 MET cc_start: 0.8690 (tpp) cc_final: 0.8435 (tpp)
REVERT: F   27 GLN cc_start: 0.9232 (mm-40) cc_final: 0.8920 (mp10)
REVERT: F   58 LEU cc_start: 0.9240 (tt) cc_final: 0.9034 (pp)
REVERT: F   63 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8099 (mt-10)
REVERT: F   88 TYR cc_start: 0.8566 (m-10) cc_final: 0.7754 (m-80)
REVERT: G   31 ARG cc_start: 0.8243 (ttm170) cc_final: 0.8029 (ttp80)
REVERT: G   35 HIS cc_start: 0.8993 (m90) cc_final: 0.8702 (m170)
REVERT: G   66 LEU cc_start: 0.8945 (mt) cc_final: 0.8651 (pp)
REVERT: G  100 ILE cc_start: 0.8629 (mp) cc_final: 0.8372 (mp)
REVERT: H  102 LEU cc_start: 0.8477 (tp) cc_final: 0.8125 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.1107
  time to fit residues: 27.7670
Evaluate side-chains
  124 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 20 optimal weight:   10.0000
   chunk 3 optimal weight:    0.5980
   chunk 9 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   chunk 82 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9980
   chunk 81 optimal weight:    7.9990
   chunk 56 optimal weight:    3.9990
   chunk 80 optimal weight:    8.9990
   overall best weight:    2.5184

-------------------------------------------------------------------------------
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 = 0.3307 r_free = 0.3307 target = 0.047975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.036499 restraints weight = 86712.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.037638 restraints weight = 49790.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.038405 restraints weight = 34605.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.038895 restraints weight = 27296.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.039207 restraints weight = 23455.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.6154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  11186  Z= 0.215
  Angle     :  0.703  10.693  16173  Z= 0.404
  Chirality :  0.039   0.236   1850
  Planarity :  0.005   0.057   1178
  Dihedral  : 34.057 170.819   3476
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 18.50
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  3.15 %
    Favored  : 96.25 %
  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 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:  0.35 (0.31), residues: 666
  helix:  1.04 (0.22), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.34 (0.42), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E  72 
 TYR   0.023   0.002   TYR H  40 
 PHE   0.019   0.002   PHE E 104 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 (11186)
  covalent geometry    : angle       0.70298 (16173)
  hydrogen bonds       : bond        0.06486 (  698)
  hydrogen bonds       : angle       3.84292 ( 1753)

*********************** 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
  177 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.8484 (mmp-170) cc_final: 0.7881 (mmp80)
REVERT: A   70 LEU cc_start: 0.9644 (pp) cc_final: 0.9419 (tt)
REVERT: B   27 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8781 (mp10)
REVERT: C   35 HIS cc_start: 0.9149 (m90) cc_final: 0.8809 (m-70)
REVERT: C   45 ARG cc_start: 0.8194 (mtm-85) cc_final: 0.7709 (mtm-85)
REVERT: C   66 LEU cc_start: 0.8898 (mt) cc_final: 0.8560 (pp)
REVERT: D  102 LEU cc_start: 0.8017 (tp) cc_final: 0.7815 (tp)
REVERT: D  105 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8437 (tm-30)
REVERT: D  109 HIS cc_start: 0.8800 (m90) cc_final: 0.8449 (m90)
REVERT: F   27 GLN cc_start: 0.9185 (mm-40) cc_final: 0.8872 (mp10)
REVERT: F   63 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8117 (mt-10)
REVERT: G   35 HIS cc_start: 0.9021 (m90) cc_final: 0.8744 (m170)
REVERT: G   66 LEU cc_start: 0.8923 (mt) cc_final: 0.8665 (pp)
REVERT: G  100 ILE cc_start: 0.8676 (mp) cc_final: 0.8444 (mp)
REVERT: H   99 ARG cc_start: 0.9383 (ttm170) cc_final: 0.9118 (ttm-80)
REVERT: H  102 LEU cc_start: 0.8536 (tp) cc_final: 0.8324 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.1111
  time to fit residues: 26.9020
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  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 87 optimal weight:    7.9990
   chunk 14 optimal weight:    1.9990
   chunk 86 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   chunk 33 optimal weight:    8.9990
   chunk 20 optimal weight:    9.9990
   chunk 8 optimal weight:    0.6980
   chunk 39 optimal weight:    0.2980
   chunk 42 optimal weight:    2.9990
   chunk 80 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.7986

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.048682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.037117 restraints weight = 86396.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.038218 restraints weight = 49416.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.038983 restraints weight = 34641.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.039493 restraints weight = 27467.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.039801 restraints weight = 23583.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.6403

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= 0.186
  Angle     :  0.687   8.830  16173  Z= 0.392
  Chirality :  0.039   0.234   1850
  Planarity :  0.005   0.058   1178
  Dihedral  : 34.005 171.702   3476
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 17.12
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  3.15 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.18 %
    Favored  : 99.65 %
  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:  0.43 (0.31), residues: 666
  helix:  1.10 (0.22), residues: 500
  sheet:  None (None), residues: 0
  loop : -2.24 (0.41), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 128 
 TYR   0.021   0.002   TYR F  88 
 PHE   0.016   0.002   PHE E 104 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (11186)
  covalent geometry    : angle       0.68685 (16173)
  hydrogen bonds       : bond        0.06003 (  698)
  hydrogen bonds       : angle       3.68278 ( 1753)

********************** 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
  171 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 170
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.7407 (mm) cc_final: 0.7168 (pp)
REVERT: A   63 ARG cc_start: 0.8506 (mmp-170) cc_final: 0.8098 (mmp80)
REVERT: A   70 LEU cc_start: 0.9646 (pp) cc_final: 0.9395 (tt)
REVERT: B   27 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8795 (mp10)
REVERT: C   35 HIS cc_start: 0.9110 (m90) cc_final: 0.8739 (m-70)
REVERT: C   45 ARG cc_start: 0.8161 (mtm-85) cc_final: 0.7780 (mtm-85)
REVERT: C   66 LEU cc_start: 0.8917 (mt) cc_final: 0.8550 (pp)
REVERT: D  102 LEU cc_start: 0.8018 (tp) cc_final: 0.7593 (tp)
REVERT: D  105 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8419 (tm-30)
REVERT: D  106 LEU cc_start: 0.9184 (mt) cc_final: 0.8970 (mt)
REVERT: D  109 HIS cc_start: 0.8796 (m90) cc_final: 0.8423 (m90)
REVERT: E  120 MET cc_start: 0.8650 (tpp) cc_final: 0.8340 (tpp)
REVERT: F   27 GLN cc_start: 0.9151 (mm-40) cc_final: 0.8784 (mp10)
REVERT: F   49 LEU cc_start: 0.8840 (mp) cc_final: 0.8117 (mp)
REVERT: F   53 GLU cc_start: 0.9372 (mm-30) cc_final: 0.9032 (mp0)
REVERT: F   63 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8073 (mt-10)
REVERT: G   66 LEU cc_start: 0.8957 (mt) cc_final: 0.8703 (pp)
REVERT: G  100 ILE cc_start: 0.8623 (mp) cc_final: 0.8380 (mp)
REVERT: H   99 ARG cc_start: 0.9373 (ttm170) cc_final: 0.9105 (ttm-80)
REVERT: H  102 LEU cc_start: 0.8592 (tp) cc_final: 0.8301 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 171
  average time/residue: 0.1091
  time to fit residues: 25.8585
Evaluate side-chains
  137 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 53 optimal weight:    9.9990
   chunk 70 optimal weight:    7.9990
   chunk 4 optimal weight:    0.8980
   chunk 60 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 85 optimal weight:    6.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3375 r_free = 0.3375 target = 0.050378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.038646 restraints weight = 85438.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.039823 restraints weight = 48875.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.040598 restraints weight = 33819.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.041139 restraints weight = 26781.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.041423 restraints weight = 22893.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.6772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11186  Z= 0.163
  Angle     :  0.670   8.824  16173  Z= 0.380
  Chirality :  0.038   0.214   1850
  Planarity :  0.005   0.063   1178
  Dihedral  : 33.791 171.994   3476
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.30 %
    Favored  : 96.40 %
  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 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:  0.50 (0.31), residues: 666
  helix:  1.09 (0.22), residues: 500
  sheet:  None (None), residues: 0
  loop : -1.96 (0.43), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 128 
 TYR   0.018   0.001   TYR F  88 
 PHE   0.013   0.002   PHE E 104 
 HIS   0.002   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (11186)
  covalent geometry    : angle       0.66989 (16173)
  hydrogen bonds       : bond        0.05558 (  698)
  hydrogen bonds       : angle       3.61608 ( 1753)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1479.31 seconds
wall clock time: 26 minutes 21.89 seconds (1581.89 seconds total)