Starting phenix.real_space_refine
on Fri Sep 11 12:38:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yoz_33991/09_2026/7yoz_33991.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yoz_33991/09_2026/7yoz_33991.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yoz_33991/09_2026/7yoz_33991.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yoz_33991/09_2026/7yoz_33991.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yoz_33991/09_2026/7yoz_33991.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yoz_33991/09_2026/7yoz_33991.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     242      5.49       5
     S      20      5.16       5
     C    5365      2.51       5
     N    1838      2.21       5
     O    2287      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9752
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 619
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "B"
      Number of atoms: 594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 594
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
    Chain: "C"
      Number of atoms: 625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 625
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
    Chain: "D"
      Number of atoms: 568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 568
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 1, 'TRANS': 69}
    Chain: "E"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 619
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "F"
      Number of atoms: 565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 565
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 1, 'TRANS': 69}
    Chain: "G"
      Number of atoms: 625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 625
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
    Chain: "H"
      Number of atoms: 576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 576
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 1, 'TRANS': 70}
    Chain: "I"
      Number of atoms: 2463
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 2463
          Classifications: {'DNA': 121}
          Link IDs: {'rna3p': 120}
    Chain: "J"
      Number of atoms: 2498
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 2498
          Classifications: {'DNA': 121}
          Link IDs: {'rna3p': 120}
  Time building chain proxies: 2.23, per 1000 atoms: 0.23
  Number of scatterers: 9752
  At special positions: 0
  Unit cell: (122.85, 90.3, 113.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      20     16.00
     P     242     15.00
     O    2287      8.00
     N    1838      7.00
     C    5365      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.97
  Conformation dependent library (CDL) restraints added in 181.9 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 2 sheets defined
      79.1% alpha, 0.7% beta
      120 base pairs and 215 stacking pairs defined.
    Time for finding SS restraints: 1.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 64 through 79
      removed outlier: 3.614A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.575A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.537A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.512A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 79
    Processing helix  chain 'C' and resid 85 through 114
    Processing helix  chain 'C' and resid 120 through 131
      removed outlier: 3.526A  pdb=" N   ILE C 124 " --> pdb=" O   MET C 120 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 25 through 29
    Processing helix  chain 'D' and resid 30 through 41
    Processing helix  chain 'D' and resid 49 through 77
    Processing helix  chain 'D' and resid 82 through 95
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.531A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.563A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.537A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 63 through 79
      removed outlier: 3.653A  pdb=" N   ASP G  77 " --> pdb=" O   GLU G  73 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   PHE G  78 " --> pdb=" O   ILE G  74 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 85 through 114
    Processing helix  chain 'G' and resid 120 through 132
      removed outlier: 3.593A  pdb=" N   ILE G 124 " --> pdb=" O   MET G 120 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 24 through 29
    Processing helix  chain 'H' and resid 30 through 41
    Processing helix  chain 'H' and resid 49 through 76
    Processing helix  chain 'H' and resid 82 through 93
    Processing sheet with id=AA1, first strand: chain 'C' and resid 118 through 119
    Processing sheet with id=AA2, first strand: chain 'G' and resid 83 through 84
      removed outlier: 7.722A  pdb=" N   ARG G  83 " --> pdb=" O   VAL H  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2

    350 hydrogen bonds defined for protein.
    1023 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      313 hydrogen bonds
      626 hydrogen bond angles
      0 basepair planarities
      120 basepair parallelities
      215 stacking parallelities
  Total time for adding SS restraints: 1.82

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1961
        1.34 -     1.45: 3358
        1.45 -     1.57: 4570
        1.57 -     1.69: 482
        1.69 -     1.81: 32
  Bond restraints: 10403
  Sorted by residual:
  bond pdb=" C3'  DT I  14 "
       pdb=" C2'  DT I  14 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.19e+01
  bond pdb=" C3'  DC I -27 "
       pdb=" C2'  DC I -27 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.11e+01
  bond pdb=" C3'  DC I  -8 "
       pdb=" C2'  DC I  -8 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.10e+01
  bond pdb=" C3'  DG J  -8 "
       pdb=" C2'  DG J  -8 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.07e+01
  bond pdb=" C3'  DA I -52 "
       pdb=" C2'  DA I -52 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.06e+01
  ... (remaining 10398 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 14297
        1.58 -     3.17: 745
        3.17 -     4.75: 17
        4.75 -     6.33: 6
        6.33 -     7.92: 3
  Bond angle restraints: 15068
  Sorted by residual:
  angle pdb=" N3   DT I  32 "
        pdb=" C4   DT I  32 "
        pdb=" O4   DT I  32 "
      ideal   model   delta    sigma   weight residual
     119.90  122.41   -2.51 6.00e-01 2.78e+00 1.76e+01
  angle pdb=" N3   DT J  13 "
        pdb=" C4   DT J  13 "
        pdb=" O4   DT J  13 "
      ideal   model   delta    sigma   weight residual
     119.90  122.39   -2.49 6.00e-01 2.78e+00 1.72e+01
  angle pdb=" N3   DT J  20 "
        pdb=" C4   DT J  20 "
        pdb=" O4   DT J  20 "
      ideal   model   delta    sigma   weight residual
     119.90  122.39   -2.49 6.00e-01 2.78e+00 1.72e+01
  angle pdb=" N3   DT I  33 "
        pdb=" C4   DT I  33 "
        pdb=" O4   DT I  33 "
      ideal   model   delta    sigma   weight residual
     119.90  122.38   -2.48 6.00e-01 2.78e+00 1.71e+01
  angle pdb=" N3   DT I  40 "
        pdb=" C4   DT I  40 "
        pdb=" O4   DT I  40 "
      ideal   model   delta    sigma   weight residual
     119.90  122.38   -2.48 6.00e-01 2.78e+00 1.70e+01
  ... (remaining 15063 not shown)

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

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1338
       0.050 -    0.101: 350
       0.101 -    0.151: 32
       0.151 -    0.201: 1
       0.201 -    0.252: 2
  Chirality restraints: 1723
  Sorted by residual:
  chirality pdb=" CG  LEU A 103 "
            pdb=" CB  LEU A 103 "
            pdb=" CD1 LEU A 103 "
            pdb=" CD2 LEU A 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.84    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CG  LEU G 103 "
            pdb=" CB  LEU G 103 "
            pdb=" CD1 LEU G 103 "
            pdb=" CD2 LEU G 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.81    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  THR G 107 "
            pdb=" N   THR G 107 "
            pdb=" C   THR G 107 "
            pdb=" CB  THR G 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.15 2.00e-01 2.50e+01 5.80e-01
  ... (remaining 1720 not shown)

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

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1872
        2.80 -     3.32: 8558
        3.32 -     3.85: 18168
        3.85 -     4.37: 20847
        4.37 -     4.90: 29311
  Nonbonded interactions: 78756
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NH2 ARG E 131 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" OD2 ASP A 106 "
            pdb=" NH2 ARG A 131 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" NZ  LYS C 115 "
            pdb=" OP2  DT J  29 "
     model   vdw
     2.324 3.120
  nonbonded pdb=" NE  ARG G 128 "
            pdb=" OE1 GLU G 133 "
     model   vdw
     2.359 3.120
  nonbonded pdb=" NZ  LYS G  79 "
            pdb=" OE1 GLU H  74 "
     model   vdw
     2.366 3.120
  ... (remaining 78751 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'C' and resid 59 through 134)
  selection = chain 'E'
  selection = (chain 'G' and resid 59 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 25 through 94)
  selection = (chain 'D' and resid 25 through 94)
  selection = (chain 'F' and resid 25 through 94)
  selection = (chain 'H' and resid 25 through 94)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.120
  Find NCS groups from input model:        0.140
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7243
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      :  0.005   0.036  10403  Z= 0.490
  Angle     :  0.724   7.918  15068  Z= 0.639
  Chirality :  0.044   0.252   1723
  Planarity :  0.004   0.050   1069
  Dihedral  : 27.407 178.984   4513
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.64 (0.30), residues: 578
  helix:  0.94 (0.21), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.23 (0.43), residues: 128

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



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00535 /  0.49 (10403)
  covalent geometry    : angle       0.72359 /  0.64 (15068)
  hydrogen bonds       : bond        0.17426 / 11.88 (  663)
  hydrogen bonds       : angle       4.78242 /  3.48 ( 1649)

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

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 335
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.8865 (tt0) cc_final: 0.8417 (tp40)
REVERT: A   85 GLN cc_start: 0.8636 (tt0) cc_final: 0.8316 (tp40)
REVERT: A   93 GLN cc_start: 0.8675 (tt0) cc_final: 0.8035 (tm-30)
REVERT: A  119 ILE cc_start: 0.9037 (pt) cc_final: 0.8294 (mt)
REVERT: A  120 MET cc_start: 0.8634 (mmm) cc_final: 0.8398 (mmm)
REVERT: A  123 ASP cc_start: 0.8834 (m-30) cc_final: 0.8470 (t70)
REVERT: A  126 LEU cc_start: 0.9647 (tp) cc_final: 0.9434 (tp)
REVERT: A  128 ARG cc_start: 0.8893 (mtp180) cc_final: 0.8319 (mtp180)
REVERT: A  130 ILE cc_start: 0.9707 (mt) cc_final: 0.9488 (mm)
REVERT: B   51 TYR cc_start: 0.8033 (m-80) cc_final: 0.7672 (m-80)
REVERT: C  104 PHE cc_start: 0.9000 (m-80) cc_final: 0.8544 (m-80)
REVERT: C  121 PRO cc_start: 0.8850 (Cg_exo) cc_final: 0.8622 (Cg_endo)
REVERT: C  123 ASP cc_start: 0.8887 (m-30) cc_final: 0.8360 (m-30)
REVERT: C  124 ILE cc_start: 0.9349 (mt) cc_final: 0.9098 (tp)
REVERT: C  130 ILE cc_start: 0.8366 (tt) cc_final: 0.8039 (tt)
REVERT: D   43 VAL cc_start: 0.8313 (t) cc_final: 0.7890 (t)
REVERT: D   52 GLU cc_start: 0.9122 (tt0) cc_final: 0.8829 (pp20)
REVERT: D   55 ARG cc_start: 0.8771 (mtt180) cc_final: 0.8373 (mmm-85)
REVERT: D   59 LYS cc_start: 0.9150 (tttt) cc_final: 0.8325 (tptt)
REVERT: D   66 ILE cc_start: 0.9140 (mm) cc_final: 0.8915 (pt)
REVERT: D   71 THR cc_start: 0.8948 (m) cc_final: 0.8446 (m)
REVERT: D   79 LYS cc_start: 0.8832 (mttt) cc_final: 0.8630 (pptt)
REVERT: E   60 LEU cc_start: 0.6207 (mt) cc_final: 0.5990 (mp)
REVERT: E   70 LEU cc_start: 0.8786 (tp) cc_final: 0.8250 (tt)
REVERT: E   87 SER cc_start: 0.8980 (m) cc_final: 0.8514 (p)
REVERT: E  104 PHE cc_start: 0.8998 (m-80) cc_final: 0.8460 (m-80)
REVERT: E  109 LEU cc_start: 0.9725 (tp) cc_final: 0.9502 (tp)
REVERT: E  126 LEU cc_start: 0.9139 (tp) cc_final: 0.8916 (tt)
REVERT: F   59 LYS cc_start: 0.9204 (tttt) cc_final: 0.8905 (ttpt)
REVERT: F   66 ILE cc_start: 0.9055 (mm) cc_final: 0.8818 (pt)
REVERT: G   70 LEU cc_start: 0.9140 (tp) cc_final: 0.8388 (tt)
REVERT: G   90 MET cc_start: 0.8385 (ttm) cc_final: 0.8053 (tmm)
REVERT: G   97 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7713 (mt-10)
REVERT: G  123 ASP cc_start: 0.8589 (m-30) cc_final: 0.8378 (t70)
REVERT: H   43 VAL cc_start: 0.6861 (t) cc_final: 0.5954 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 335
  average time/residue: 0.1632
  time to fit residues: 67.6628
Evaluate side-chains
  222 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:   30.0000
   chunk 62 optimal weight:   30.0000
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:   30.0000
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:   30.0000
   overall best weight:    2.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  68 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.091023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.076814 restraints weight = 54888.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.078423 restraints weight = 33933.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.079583 restraints weight = 23873.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.080341 restraints weight = 18369.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.080867 restraints weight = 15237.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076  10403  Z= 0.202
  Angle     :  0.715   8.167  15068  Z= 0.419
  Chirality :  0.044   0.244   1723
  Planarity :  0.007   0.094   1069
  Dihedral  : 31.290 174.462   3286
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 19.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  3.57 %
    Favored  : 95.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.63 (0.33), residues: 578
  helix:  1.63 (0.23), residues: 465
  sheet:  None (None), residues: 0
  loop : -1.16 (0.49), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG F  78 
 TYR   0.021   0.002   TYR D  72 
 PHE   0.016   0.002   PHE E  67 
 HIS   0.018   0.004   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00378 /  0.20 (10403)
  covalent geometry    : angle       0.71472 /  0.42 (15068)
  hydrogen bonds       : bond        0.07179 /  4.85 (  663)
  hydrogen bonds       : angle       3.41389 /  2.40 ( 1649)

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

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 255
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 LEU cc_start: 0.8261 (tt) cc_final: 0.6978 (tt)
REVERT: A   68 GLN cc_start: 0.9016 (tt0) cc_final: 0.8801 (tp-100)
REVERT: A   85 GLN cc_start: 0.9005 (tt0) cc_final: 0.8644 (mm110)
REVERT: A   93 GLN cc_start: 0.8804 (tt0) cc_final: 0.8524 (tt0)
REVERT: A   96 CYS cc_start: 0.8940 (m) cc_final: 0.8701 (m)
REVERT: A   97 GLU cc_start: 0.8181 (tt0) cc_final: 0.7569 (mt-10)
REVERT: A  107 THR cc_start: 0.8889 (p) cc_final: 0.8624 (p)
REVERT: A  123 ASP cc_start: 0.8881 (m-30) cc_final: 0.8417 (t70)
REVERT: A  130 ILE cc_start: 0.9749 (mt) cc_final: 0.9475 (mm)
REVERT: B   24 ASP cc_start: 0.8094 (t0) cc_final: 0.7396 (p0)
REVERT: B   51 TYR cc_start: 0.8312 (m-80) cc_final: 0.8032 (m-80)
REVERT: C   90 MET cc_start: 0.9077 (ppp) cc_final: 0.8574 (ppp)
REVERT: C   93 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8717 (tm-30)
REVERT: C   94 GLU cc_start: 0.9175 (pt0) cc_final: 0.8765 (pt0)
REVERT: C  100 LEU cc_start: 0.9382 (tp) cc_final: 0.9151 (tp)
REVERT: C  104 PHE cc_start: 0.9016 (m-80) cc_final: 0.8491 (m-80)
REVERT: C  106 ASP cc_start: 0.9195 (m-30) cc_final: 0.8522 (m-30)
REVERT: D   52 GLU cc_start: 0.9111 (tt0) cc_final: 0.8799 (tm-30)
REVERT: D   59 LYS cc_start: 0.9092 (tttt) cc_final: 0.8313 (tptp)
REVERT: D   66 ILE cc_start: 0.9077 (mm) cc_final: 0.8839 (pt)
REVERT: E   70 LEU cc_start: 0.8649 (tp) cc_final: 0.7967 (mt)
REVERT: E   83 ARG cc_start: 0.5466 (ptt-90) cc_final: 0.5195 (ptt-90)
REVERT: E   87 SER cc_start: 0.8765 (m) cc_final: 0.8428 (p)
REVERT: E  123 ASP cc_start: 0.8967 (m-30) cc_final: 0.8735 (m-30)
REVERT: F   59 LYS cc_start: 0.9194 (tttt) cc_final: 0.8902 (ttpt)
REVERT: F   66 ILE cc_start: 0.9094 (mm) cc_final: 0.8874 (pt)
REVERT: G   61 LEU cc_start: 0.8460 (tt) cc_final: 0.8139 (tt)
REVERT: G   90 MET cc_start: 0.8509 (ttm) cc_final: 0.8249 (tmm)
REVERT: G  120 MET cc_start: 0.8932 (mmp) cc_final: 0.8731 (mmm)
REVERT: G  123 ASP cc_start: 0.8679 (m-30) cc_final: 0.8257 (t70)
REVERT: G  125 GLN cc_start: 0.9059 (tp40) cc_final: 0.8837 (tp40)
REVERT: G  128 ARG cc_start: 0.9180 (mtp-110) cc_final: 0.8973 (mtp-110)
  outliers start: 5
  outliers final: 2
  residues processed: 256
  average time/residue: 0.1385
  time to fit residues: 45.5644
Evaluate side-chains
  205 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 203
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:   40.0000
   chunk 44 optimal weight:    8.9990
   chunk 78 optimal weight:   40.0000
   chunk 28 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 17 optimal weight:    5.9990
   chunk 76 optimal weight:   30.0000
   chunk 46 optimal weight:    0.8980
   chunk 65 optimal weight:   30.0000
   chunk 20 optimal weight:    8.9990
   chunk 63 optimal weight:   30.0000
   overall best weight:    3.5786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 125 GLN
F  25 ASN
F  27 GLN
** G  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.086187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.071686 restraints weight = 55398.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.073200 restraints weight = 34313.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.074274 restraints weight = 24334.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.074973 restraints weight = 18900.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.075471 restraints weight = 15870.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.4254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079  10403  Z= 0.211
  Angle     :  0.745  13.183  15068  Z= 0.423
  Chirality :  0.048   0.444   1723
  Planarity :  0.008   0.122   1069
  Dihedral  : 31.786 176.985   3286
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 16.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  6.75 %
    Favored  : 92.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.56 (0.33), residues: 578
  helix:  1.61 (0.23), residues: 465
  sheet:  None (None), residues: 0
  loop : -1.32 (0.47), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.032   0.001   ARG A 128 
 TYR   0.013   0.002   TYR H  51 
 PHE   0.028   0.002   PHE E  67 
 HIS   0.007   0.002   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00404 /  0.21 (10403)
  covalent geometry    : angle       0.74500 /  0.42 (15068)
  hydrogen bonds       : bond        0.06622 /  4.48 (  663)
  hydrogen bonds       : angle       3.36692 /  2.34 ( 1649)

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

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 248
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 LEU cc_start: 0.8254 (tt) cc_final: 0.7904 (tt)
REVERT: A   64 LYS cc_start: 0.9132 (mtmt) cc_final: 0.8495 (mtmm)
REVERT: A   85 GLN cc_start: 0.9106 (tt0) cc_final: 0.8766 (mm110)
REVERT: A   93 GLN cc_start: 0.8882 (tt0) cc_final: 0.8621 (pt0)
REVERT: A   96 CYS cc_start: 0.8833 (m) cc_final: 0.8608 (p)
REVERT: A  107 THR cc_start: 0.9019 (p) cc_final: 0.8705 (p)
REVERT: A  119 ILE cc_start: 0.9170 (mt) cc_final: 0.8773 (mt)
REVERT: A  123 ASP cc_start: 0.8946 (m-30) cc_final: 0.8405 (t70)
REVERT: A  130 ILE cc_start: 0.9813 (mt) cc_final: 0.9465 (mm)
REVERT: B   24 ASP cc_start: 0.8103 (t0) cc_final: 0.7577 (p0)
REVERT: C   90 MET cc_start: 0.9137 (ppp) cc_final: 0.8584 (ppp)
REVERT: C   93 GLN cc_start: 0.8967 (tm-30) cc_final: 0.8679 (tm-30)
REVERT: C   94 GLU cc_start: 0.9181 (pt0) cc_final: 0.8759 (pt0)
REVERT: C  104 PHE cc_start: 0.9035 (m-80) cc_final: 0.8605 (m-80)
REVERT: C  106 ASP cc_start: 0.8827 (m-30) cc_final: 0.8614 (m-30)
REVERT: C  129 ARG cc_start: 0.8305 (tpm170) cc_final: 0.7788 (tpm170)
REVERT: D   35 ARG cc_start: 0.9052 (mmm-85) cc_final: 0.8810 (mmm-85)
REVERT: D   55 ARG cc_start: 0.8803 (mtt180) cc_final: 0.8331 (mmm-85)
REVERT: D   59 LYS cc_start: 0.9194 (tttt) cc_final: 0.8438 (tptp)
REVERT: D   63 GLU cc_start: 0.8786 (tt0) cc_final: 0.8269 (tm-30)
REVERT: D   66 ILE cc_start: 0.9113 (mm) cc_final: 0.8850 (pt)
REVERT: D   84 MET cc_start: 0.8638 (tpt) cc_final: 0.8417 (mmm)
REVERT: D   90 LEU cc_start: 0.8555 (mt) cc_final: 0.8347 (mt)
REVERT: E   76 GLN cc_start: 0.8575 (tt0) cc_final: 0.8214 (tp-100)
REVERT: E   87 SER cc_start: 0.8800 (m) cc_final: 0.8332 (p)
REVERT: E  119 ILE cc_start: 0.7922 (pt) cc_final: 0.7593 (pt)
REVERT: F   36 ARG cc_start: 0.8883 (mtm110) cc_final: 0.8656 (ttp80)
REVERT: F   59 LYS cc_start: 0.9275 (tttt) cc_final: 0.9053 (ttpt)
REVERT: F   63 GLU cc_start: 0.8821 (tt0) cc_final: 0.8548 (tm-30)
REVERT: F   66 ILE cc_start: 0.9090 (mm) cc_final: 0.8850 (pt)
REVERT: F   90 LEU cc_start: 0.8933 (tt) cc_final: 0.8620 (pp)
REVERT: G   90 MET cc_start: 0.8579 (ttm) cc_final: 0.8348 (tmm)
REVERT: G   92 LEU cc_start: 0.9541 (mm) cc_final: 0.9309 (mm)
REVERT: G  123 ASP cc_start: 0.8721 (m-30) cc_final: 0.8261 (t70)
REVERT: G  128 ARG cc_start: 0.9157 (mtp-110) cc_final: 0.8936 (mtp-110)
REVERT: H   78 ARG cc_start: 0.8377 (ptp90) cc_final: 0.8102 (ptp90)
REVERT: H   84 MET cc_start: 0.8907 (ttm) cc_final: 0.8650 (ttt)
REVERT: H   85 ASP cc_start: 0.8439 (m-30) cc_final: 0.8235 (m-30)
  outliers start: 4
  outliers final: 0
  residues processed: 249
  average time/residue: 0.1304
  time to fit residues: 42.0667
Evaluate side-chains
  211 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 8 optimal weight:    4.9990
   chunk 57 optimal weight:   50.0000
   chunk 35 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 67 optimal weight:   50.0000
   chunk 61 optimal weight:   30.0000
   chunk 78 optimal weight:   40.0000
   chunk 70 optimal weight:   30.0000
   chunk 62 optimal weight:   30.0000
   chunk 64 optimal weight:   30.0000
   overall best weight:   10.7992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 113 HIS
** C  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 113 HIS
** G  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  75 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.065205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.049946 restraints weight = 59553.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.051305 restraints weight = 35902.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.052249 restraints weight = 25567.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.052877 restraints weight = 20154.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.053300 restraints weight = 17092.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.8047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.105  10403  Z= 0.450
  Angle     :  1.181  18.232  15068  Z= 0.639
  Chirality :  0.064   0.349   1723
  Planarity :  0.011   0.106   1069
  Dihedral  : 32.941 179.603   3286
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 35.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 10.12 %
    Favored  : 89.29 %
  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: -0.92 (0.32), residues: 578
  helix: -0.17 (0.23), residues: 465
  sheet:  None (None), residues: 0
  loop : -1.99 (0.45), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.002   ARG E  63 
 TYR   0.020   0.004   TYR F  72 
 PHE   0.072   0.006   PHE C 104 
 HIS   0.017   0.006   HIS H  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00883 /  0.45 (10403)
  covalent geometry    : angle       1.18071 /  0.64 (15068)
  hydrogen bonds       : bond        0.14255 /  9.73 (  663)
  hydrogen bonds       : angle       5.07492 /  3.61 ( 1649)

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

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 267
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 THR cc_start: 0.9716 (p) cc_final: 0.9502 (p)
REVERT: A  123 ASP cc_start: 0.8963 (m-30) cc_final: 0.8739 (t70)
REVERT: A  128 ARG cc_start: 0.8704 (ttt90) cc_final: 0.8477 (mmm160)
REVERT: A  133 GLU cc_start: 0.9076 (tt0) cc_final: 0.8830 (tt0)
REVERT: B   24 ASP cc_start: 0.8571 (t0) cc_final: 0.8300 (t0)
REVERT: B   52 GLU cc_start: 0.8981 (tp30) cc_final: 0.8748 (tp30)
REVERT: B   74 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8167 (tm-30)
REVERT: B   85 ASP cc_start: 0.9180 (m-30) cc_final: 0.8922 (m-30)
REVERT: C   90 MET cc_start: 0.9153 (ppp) cc_final: 0.8543 (ppp)
REVERT: C   93 GLN cc_start: 0.9256 (tm-30) cc_final: 0.9033 (tm-30)
REVERT: C   94 GLU cc_start: 0.9300 (pt0) cc_final: 0.8859 (pt0)
REVERT: C  129 ARG cc_start: 0.8728 (tpm170) cc_final: 0.8480 (tpm170)
REVERT: D   55 ARG cc_start: 0.9155 (mtt180) cc_final: 0.8577 (mmm-85)
REVERT: D   59 LYS cc_start: 0.9450 (tttt) cc_final: 0.8761 (tptp)
REVERT: D   63 GLU cc_start: 0.9134 (tt0) cc_final: 0.8884 (tm-30)
REVERT: D   64 ASN cc_start: 0.9141 (t0) cc_final: 0.8794 (t0)
REVERT: D   72 TYR cc_start: 0.8285 (t80) cc_final: 0.8042 (t80)
REVERT: E   76 GLN cc_start: 0.8833 (tt0) cc_final: 0.8295 (tp-100)
REVERT: E   90 MET cc_start: 0.8782 (ppp) cc_final: 0.8296 (ppp)
REVERT: E   93 GLN cc_start: 0.9215 (mm110) cc_final: 0.8170 (tp40)
REVERT: E  106 ASP cc_start: 0.9311 (t0) cc_final: 0.9071 (t70)
REVERT: E  119 ILE cc_start: 0.8542 (pt) cc_final: 0.8266 (pt)
REVERT: E  123 ASP cc_start: 0.9043 (m-30) cc_final: 0.8222 (m-30)
REVERT: F   64 ASN cc_start: 0.9176 (t0) cc_final: 0.8902 (t0)
REVERT: F   82 THR cc_start: 0.8175 (p) cc_final: 0.7967 (t)
REVERT: G   90 MET cc_start: 0.8876 (ttm) cc_final: 0.8550 (tmm)
REVERT: G  107 THR cc_start: 0.9699 (p) cc_final: 0.9366 (p)
REVERT: G  123 ASP cc_start: 0.8885 (m-30) cc_final: 0.8512 (t70)
REVERT: G  128 ARG cc_start: 0.9226 (mtp-110) cc_final: 0.8914 (mtp-110)
REVERT: H   55 ARG cc_start: 0.9174 (mtt-85) cc_final: 0.8555 (mtt-85)
REVERT: H   63 GLU cc_start: 0.8638 (tt0) cc_final: 0.8242 (mm-30)
REVERT: H   72 TYR cc_start: 0.9060 (m-80) cc_final: 0.8801 (m-10)
  outliers start: 3
  outliers final: 1
  residues processed: 267
  average time/residue: 0.1296
  time to fit residues: 44.9914
Evaluate side-chains
  225 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 224
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 77 optimal weight:   30.0000
   chunk 39 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 76 optimal weight:   30.0000
   chunk 31 optimal weight:    5.9990
   chunk 69 optimal weight:   40.0000
   chunk 54 optimal weight:    6.9990
   chunk 27 optimal weight:    8.9990
   chunk 21 optimal weight:    8.9990
   chunk 57 optimal weight:   40.0000
   chunk 49 optimal weight:    0.8980
   overall best weight:    5.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  75 HIS
F  25 ASN
** G  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.066868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.051883 restraints weight = 60418.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.053229 restraints weight = 36353.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.054140 restraints weight = 25751.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.054770 restraints weight = 20310.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.055131 restraints weight = 17254.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.8354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.079  10403  Z= 0.231
  Angle     :  0.817   9.709  15068  Z= 0.461
  Chirality :  0.053   0.292   1723
  Planarity :  0.007   0.096   1069
  Dihedral  : 33.252 176.743   3286
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 19.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.32), residues: 578
  helix:  0.71 (0.23), residues: 465
  sheet:  None (None), residues: 0
  loop : -1.91 (0.45), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  35 
 TYR   0.035   0.002   TYR D  72 
 PHE   0.054   0.003   PHE C 104 
 HIS   0.009   0.002   HIS D  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00451 /  0.23 (10403)
  covalent geometry    : angle       0.81743 /  0.46 (15068)
  hydrogen bonds       : bond        0.06645 /  4.45 (  663)
  hydrogen bonds       : angle       3.88164 /  2.75 ( 1649)

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

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 277
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 LEU cc_start: 0.9057 (tt) cc_final: 0.8451 (tp)
REVERT: A   68 GLN cc_start: 0.9425 (tt0) cc_final: 0.9159 (tm-30)
REVERT: A   92 LEU cc_start: 0.9623 (mm) cc_final: 0.9140 (mm)
REVERT: A   93 GLN cc_start: 0.9278 (mt0) cc_final: 0.8686 (mt0)
REVERT: A   94 GLU cc_start: 0.8864 (pt0) cc_final: 0.8366 (pt0)
REVERT: A   97 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7680 (mt-10)
REVERT: A  125 GLN cc_start: 0.9074 (tp40) cc_final: 0.8346 (tm-30)
REVERT: A  130 ILE cc_start: 0.9793 (mt) cc_final: 0.9394 (tt)
REVERT: A  133 GLU cc_start: 0.9052 (tt0) cc_final: 0.8229 (tt0)
REVERT: B   25 ASN cc_start: 0.8324 (p0) cc_final: 0.7249 (p0)
REVERT: B   35 ARG cc_start: 0.8833 (ttm110) cc_final: 0.8470 (ttm110)
REVERT: B   74 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8218 (tm-30)
REVERT: C   78 PHE cc_start: 0.8477 (t80) cc_final: 0.8085 (t80)
REVERT: C   90 MET cc_start: 0.9063 (ppp) cc_final: 0.8389 (ppp)
REVERT: C   94 GLU cc_start: 0.9306 (pt0) cc_final: 0.8748 (pt0)
REVERT: C  123 ASP cc_start: 0.9308 (m-30) cc_final: 0.9064 (m-30)
REVERT: D   55 ARG cc_start: 0.9121 (mtt180) cc_final: 0.8515 (mmm-85)
REVERT: D   63 GLU cc_start: 0.9160 (tt0) cc_final: 0.8562 (tm-30)
REVERT: D   64 ASN cc_start: 0.9033 (t0) cc_final: 0.8832 (t0)
REVERT: D   66 ILE cc_start: 0.9487 (mt) cc_final: 0.9265 (pt)
REVERT: E   76 GLN cc_start: 0.8892 (tt0) cc_final: 0.8288 (tp-100)
REVERT: E   90 MET cc_start: 0.8752 (ppp) cc_final: 0.8337 (ppp)
REVERT: E   94 GLU cc_start: 0.8949 (pt0) cc_final: 0.8329 (pt0)
REVERT: E  123 ASP cc_start: 0.8985 (m-30) cc_final: 0.8672 (m-30)
REVERT: F   60 VAL cc_start: 0.9065 (p) cc_final: 0.8464 (p)
REVERT: F   64 ASN cc_start: 0.9095 (t0) cc_final: 0.8854 (t0)
REVERT: F   66 ILE cc_start: 0.9358 (mm) cc_final: 0.9093 (pt)
REVERT: G   73 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8873 (tm-30)
REVERT: G   90 MET cc_start: 0.8791 (ttm) cc_final: 0.8296 (tmm)
REVERT: G  106 ASP cc_start: 0.9076 (t70) cc_final: 0.8793 (t70)
REVERT: G  128 ARG cc_start: 0.9204 (mtp-110) cc_final: 0.8333 (mtp-110)
REVERT: H   63 GLU cc_start: 0.8495 (tt0) cc_final: 0.7947 (tp30)
REVERT: H   88 TYR cc_start: 0.8782 (m-10) cc_final: 0.8452 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 277
  average time/residue: 0.1279
  time to fit residues: 46.1908
Evaluate side-chains
  229 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 64 optimal weight:   30.0000
   chunk 79 optimal weight:   50.0000
   chunk 30 optimal weight:    7.9990
   chunk 4 optimal weight:    0.1980
   chunk 39 optimal weight:    2.9990
   chunk 61 optimal weight:   30.0000
   chunk 46 optimal weight:    0.9980
   overall best weight:    1.8184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
** G  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.068029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.052957 restraints weight = 59407.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.054315 restraints weight = 35697.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.055272 restraints weight = 25333.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.055880 restraints weight = 19933.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.056310 restraints weight = 17020.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.8495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068  10403  Z= 0.176
  Angle     :  0.766   9.408  15068  Z= 0.430
  Chirality :  0.048   0.276   1723
  Planarity :  0.006   0.066   1069
  Dihedral  : 32.985 175.219   3286
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 16.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  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:  0.66 (0.33), residues: 578
  helix:  1.02 (0.23), residues: 466
  sheet:  None (None), residues: 0
  loop : -1.89 (0.43), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H  35 
 TYR   0.022   0.002   TYR D  72 
 PHE   0.043   0.003   PHE C 104 
 HIS   0.007   0.002   HIS H  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.18 (10403)
  covalent geometry    : angle       0.76554 /  0.43 (15068)
  hydrogen bonds       : bond        0.05453 /  3.66 (  663)
  hydrogen bonds       : angle       3.49515 /  2.47 ( 1649)

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

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 280
  time to evaluate  : 0.256 
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   85 GLN cc_start: 0.9218 (mt0) cc_final: 0.8699 (mt0)
REVERT: A  107 THR cc_start: 0.9676 (p) cc_final: 0.8916 (p)
REVERT: A  123 ASP cc_start: 0.8869 (m-30) cc_final: 0.8357 (t70)
REVERT: A  125 GLN cc_start: 0.9058 (tp40) cc_final: 0.8279 (tm-30)
REVERT: B   24 ASP cc_start: 0.8394 (t70) cc_final: 0.7921 (p0)
REVERT: B   35 ARG cc_start: 0.8707 (ttm110) cc_final: 0.8173 (ttm110)
REVERT: B   67 ARG cc_start: 0.9155 (ttm170) cc_final: 0.8817 (ttp-170)
REVERT: B   85 ASP cc_start: 0.9209 (m-30) cc_final: 0.8946 (m-30)
REVERT: C   78 PHE cc_start: 0.8424 (t80) cc_final: 0.8033 (t80)
REVERT: C   87 SER cc_start: 0.8772 (p) cc_final: 0.8571 (p)
REVERT: C   90 MET cc_start: 0.9013 (ppp) cc_final: 0.8229 (ppp)
REVERT: C   93 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8685 (tm-30)
REVERT: C   94 GLU cc_start: 0.9236 (pt0) cc_final: 0.8733 (pt0)
REVERT: C   97 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8609 (pp20)
REVERT: C  123 ASP cc_start: 0.9326 (m-30) cc_final: 0.9108 (m-30)
REVERT: D   54 THR cc_start: 0.9494 (m) cc_final: 0.9187 (p)
REVERT: D   55 ARG cc_start: 0.9094 (mtt180) cc_final: 0.8525 (mmm-85)
REVERT: D   63 GLU cc_start: 0.9116 (tt0) cc_final: 0.8556 (tm-30)
REVERT: D   66 ILE cc_start: 0.9308 (mt) cc_final: 0.9067 (pt)
REVERT: E   70 LEU cc_start: 0.9280 (mt) cc_final: 0.8685 (mm)
REVERT: E   76 GLN cc_start: 0.8984 (tt0) cc_final: 0.8378 (tp-100)
REVERT: E   87 SER cc_start: 0.8664 (p) cc_final: 0.8425 (p)
REVERT: E   90 MET cc_start: 0.8761 (ppp) cc_final: 0.8299 (ppp)
REVERT: E   94 GLU cc_start: 0.8937 (pt0) cc_final: 0.8271 (pt0)
REVERT: E  110 CYS cc_start: 0.8681 (t) cc_final: 0.7353 (t)
REVERT: E  123 ASP cc_start: 0.8983 (m-30) cc_final: 0.8010 (m-30)
REVERT: F   55 ARG cc_start: 0.9189 (mtt90) cc_final: 0.8460 (mtp180)
REVERT: F   60 VAL cc_start: 0.8979 (p) cc_final: 0.8463 (p)
REVERT: F   64 ASN cc_start: 0.9027 (t0) cc_final: 0.8818 (t0)
REVERT: F   66 ILE cc_start: 0.9404 (mm) cc_final: 0.9118 (pt)
REVERT: F   84 MET cc_start: 0.8471 (ptt) cc_final: 0.8137 (ptt)
REVERT: F   85 ASP cc_start: 0.7745 (m-30) cc_final: 0.6889 (m-30)
REVERT: F   90 LEU cc_start: 0.8951 (tt) cc_final: 0.8685 (pp)
REVERT: G   90 MET cc_start: 0.8785 (ttm) cc_final: 0.8196 (tmm)
REVERT: G  128 ARG cc_start: 0.9147 (mtp-110) cc_final: 0.8319 (mtp-110)
REVERT: H   84 MET cc_start: 0.8897 (ttm) cc_final: 0.8693 (ttm)
REVERT: H   92 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7655 (ttp80)
  outliers start: 0
  outliers final: 0
  residues processed: 280
  average time/residue: 0.1344
  time to fit residues: 48.9745
Evaluate side-chains
  229 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 29 optimal weight:    8.9990
   chunk 68 optimal weight:   50.0000
   chunk 15 optimal weight:    0.9980
   chunk 12 optimal weight:    6.9990
   chunk 70 optimal weight:   30.0000
   chunk 53 optimal weight:    0.8980
   chunk 58 optimal weight:   30.0000
   chunk 59 optimal weight:   30.0000
   chunk 20 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.9784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
G 108 ASN
** H  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.067829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.052977 restraints weight = 58631.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.054339 restraints weight = 35256.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.055301 restraints weight = 25041.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.055955 restraints weight = 19695.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.056303 restraints weight = 16670.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.8633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  10403  Z= 0.169
  Angle     :  0.737   9.371  15068  Z= 0.417
  Chirality :  0.048   0.276   1723
  Planarity :  0.005   0.067   1069
  Dihedral  : 32.823 175.719   3286
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 16.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  2.18 %
    Favored  : 97.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.91 (0.33), residues: 578
  helix:  1.20 (0.23), residues: 462
  sheet:  None (None), residues: 0
  loop : -1.69 (0.44), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG H  35 
 TYR   0.020   0.002   TYR D  72 
 PHE   0.028   0.003   PHE G 104 
 HIS   0.005   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.17 (10403)
  covalent geometry    : angle       0.73685 /  0.42 (15068)
  hydrogen bonds       : bond        0.05088 /  3.40 (  663)
  hydrogen bonds       : angle       3.34333 /  2.37 ( 1649)

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

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 266
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9430 (mtmt) cc_final: 0.8997 (mtmm)
REVERT: A   65 LEU cc_start: 0.9561 (tp) cc_final: 0.9335 (tp)
REVERT: A   92 LEU cc_start: 0.9594 (mm) cc_final: 0.9036 (mm)
REVERT: A  106 ASP cc_start: 0.9104 (t70) cc_final: 0.8894 (t70)
REVERT: A  125 GLN cc_start: 0.9072 (tp40) cc_final: 0.8305 (tm-30)
REVERT: A  133 GLU cc_start: 0.8535 (tt0) cc_final: 0.8150 (tt0)
REVERT: B   85 ASP cc_start: 0.9257 (m-30) cc_final: 0.9004 (m-30)
REVERT: C   78 PHE cc_start: 0.8423 (t80) cc_final: 0.8044 (t80)
REVERT: C   87 SER cc_start: 0.8769 (p) cc_final: 0.8569 (p)
REVERT: C   90 MET cc_start: 0.8969 (ppp) cc_final: 0.8223 (ppp)
REVERT: C   94 GLU cc_start: 0.9228 (pt0) cc_final: 0.8679 (pt0)
REVERT: C   97 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8647 (pp20)
REVERT: C  123 ASP cc_start: 0.9347 (m-30) cc_final: 0.9051 (m-30)
REVERT: D   54 THR cc_start: 0.9466 (m) cc_final: 0.9156 (p)
REVERT: D   55 ARG cc_start: 0.9080 (mtt180) cc_final: 0.8455 (mmm-85)
REVERT: D   63 GLU cc_start: 0.9137 (tt0) cc_final: 0.8712 (tm-30)
REVERT: D   66 ILE cc_start: 0.9289 (mt) cc_final: 0.9082 (pt)
REVERT: E   76 GLN cc_start: 0.9007 (tt0) cc_final: 0.8411 (tp-100)
REVERT: E   90 MET cc_start: 0.8732 (ppp) cc_final: 0.8306 (ppp)
REVERT: E   94 GLU cc_start: 0.8866 (pt0) cc_final: 0.8170 (pt0)
REVERT: E  110 CYS cc_start: 0.8592 (t) cc_final: 0.7788 (t)
REVERT: E  123 ASP cc_start: 0.8944 (m-30) cc_final: 0.8518 (m-30)
REVERT: F   55 ARG cc_start: 0.9093 (mtt90) cc_final: 0.8425 (mtp180)
REVERT: F   60 VAL cc_start: 0.9033 (p) cc_final: 0.8468 (p)
REVERT: F   64 ASN cc_start: 0.9043 (t0) cc_final: 0.8799 (t0)
REVERT: F   66 ILE cc_start: 0.9398 (mm) cc_final: 0.9114 (pt)
REVERT: F   84 MET cc_start: 0.8554 (ptt) cc_final: 0.8313 (ptt)
REVERT: F   85 ASP cc_start: 0.7846 (m-30) cc_final: 0.6776 (m-30)
REVERT: F   90 LEU cc_start: 0.9012 (tt) cc_final: 0.8686 (pp)
REVERT: G   61 LEU cc_start: 0.8986 (tt) cc_final: 0.8514 (tt)
REVERT: G   64 LYS cc_start: 0.9218 (pttt) cc_final: 0.8997 (pttm)
REVERT: G   90 MET cc_start: 0.8754 (ttm) cc_final: 0.8161 (tmm)
REVERT: G   93 GLN cc_start: 0.9115 (mm-40) cc_final: 0.8558 (mm-40)
REVERT: G   94 GLU cc_start: 0.8812 (pt0) cc_final: 0.8609 (pt0)
REVERT: G   97 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7490 (mt-10)
REVERT: G  123 ASP cc_start: 0.9149 (m-30) cc_final: 0.8898 (m-30)
REVERT: G  128 ARG cc_start: 0.9148 (mtp-110) cc_final: 0.8357 (mtp-110)
REVERT: H   92 ARG cc_start: 0.8001 (ttp80) cc_final: 0.7706 (ttp80)
  outliers start: 1
  outliers final: 0
  residues processed: 267
  average time/residue: 0.1243
  time to fit residues: 43.8105
Evaluate side-chains
  225 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 9 optimal weight:   10.0000
   chunk 56 optimal weight:   50.0000
   chunk 40 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 57 optimal weight:   40.0000
   chunk 50 optimal weight:    5.9990
   chunk 74 optimal weight:   30.0000
   chunk 42 optimal weight:    8.9990
   chunk 11 optimal weight:    0.9980
   chunk 29 optimal weight:   10.0000
   overall best weight:    4.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
A  93 GLN
G  68 GLN
** H  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.065683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.051188 restraints weight = 58905.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 18)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.052574 restraints weight = 34320.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.053547 restraints weight = 23881.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.054204 restraints weight = 18506.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.054680 restraints weight = 15498.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.8970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10403  Z= 0.211
  Angle     :  0.774  13.748  15068  Z= 0.436
  Chirality :  0.048   0.291   1723
  Planarity :  0.006   0.052   1069
  Dihedral  : 32.827 176.238   3286
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 19.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  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:  0.55 (0.32), residues: 578
  helix:  0.90 (0.23), residues: 464
  sheet:  None (None), residues: 0
  loop : -1.65 (0.45), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B  35 
 TYR   0.027   0.002   TYR F  51 
 PHE   0.037   0.003   PHE A  78 
 HIS   0.004   0.002   HIS G 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00416 /  0.21 (10403)
  covalent geometry    : angle       0.77442 /  0.44 (15068)
  hydrogen bonds       : bond        0.05956 /  3.99 (  663)
  hydrogen bonds       : angle       3.57436 /  2.52 ( 1649)

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

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 0.244 
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   65 LEU cc_start: 0.9596 (tp) cc_final: 0.9394 (tp)
REVERT: A   85 GLN cc_start: 0.9319 (mt0) cc_final: 0.8689 (mt0)
REVERT: A  106 ASP cc_start: 0.9157 (t70) cc_final: 0.8908 (t70)
REVERT: A  125 GLN cc_start: 0.9133 (tp40) cc_final: 0.8349 (tm-30)
REVERT: A  126 LEU cc_start: 0.9729 (tt) cc_final: 0.9524 (tt)
REVERT: B   67 ARG cc_start: 0.9188 (ttm170) cc_final: 0.8946 (ttp-170)
REVERT: B   74 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8347 (tm-30)
REVERT: B   85 ASP cc_start: 0.9270 (m-30) cc_final: 0.8994 (m-30)
REVERT: C   78 PHE cc_start: 0.8575 (t80) cc_final: 0.8175 (t80)
REVERT: C   90 MET cc_start: 0.8981 (ppp) cc_final: 0.8320 (ppp)
REVERT: C   94 GLU cc_start: 0.9227 (pt0) cc_final: 0.8636 (pt0)
REVERT: C  123 ASP cc_start: 0.9386 (m-30) cc_final: 0.9061 (m-30)
REVERT: D   54 THR cc_start: 0.9445 (m) cc_final: 0.9132 (p)
REVERT: D   55 ARG cc_start: 0.9090 (mtt180) cc_final: 0.8626 (mtt-85)
REVERT: D   63 GLU cc_start: 0.9135 (tt0) cc_final: 0.8719 (tm-30)
REVERT: D   66 ILE cc_start: 0.9346 (mt) cc_final: 0.9120 (pt)
REVERT: E   76 GLN cc_start: 0.9013 (tt0) cc_final: 0.8394 (tp-100)
REVERT: E   90 MET cc_start: 0.8746 (ppp) cc_final: 0.8329 (ppp)
REVERT: E  110 CYS cc_start: 0.8806 (t) cc_final: 0.8130 (t)
REVERT: E  123 ASP cc_start: 0.8981 (m-30) cc_final: 0.8652 (m-30)
REVERT: F   55 ARG cc_start: 0.9106 (mtt90) cc_final: 0.8436 (mtt-85)
REVERT: F   60 VAL cc_start: 0.9007 (p) cc_final: 0.8532 (p)
REVERT: F   63 GLU cc_start: 0.9250 (pp20) cc_final: 0.8984 (pp20)
REVERT: F   64 ASN cc_start: 0.9025 (t0) cc_final: 0.8795 (t0)
REVERT: F   66 ILE cc_start: 0.9424 (mm) cc_final: 0.9160 (pt)
REVERT: F   85 ASP cc_start: 0.7842 (m-30) cc_final: 0.7587 (m-30)
REVERT: F   90 LEU cc_start: 0.9025 (tt) cc_final: 0.8743 (pp)
REVERT: G   90 MET cc_start: 0.8831 (ttm) cc_final: 0.8068 (tmm)
REVERT: G   96 CYS cc_start: 0.8769 (m) cc_final: 0.8565 (m)
REVERT: G  120 MET cc_start: 0.9397 (mmp) cc_final: 0.9136 (mmm)
REVERT: G  123 ASP cc_start: 0.9161 (m-30) cc_final: 0.8929 (m-30)
REVERT: G  128 ARG cc_start: 0.9116 (mtp-110) cc_final: 0.8236 (mtp-110)
REVERT: H   63 GLU cc_start: 0.8526 (tt0) cc_final: 0.8127 (mm-30)
REVERT: H   95 ARG cc_start: 0.3700 (mpp-170) cc_final: 0.3444 (mpp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 262
  average time/residue: 0.1278
  time to fit residues: 43.6096
Evaluate side-chains
  224 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 62 optimal weight:   30.0000
   chunk 72 optimal weight:   30.0000
   chunk 44 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 31 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    7.9990
   chunk 77 optimal weight:   30.0000
   chunk 24 optimal weight:    8.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** G  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.063574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.049141 restraints weight = 58727.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.050500 restraints weight = 34440.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.051454 restraints weight = 24127.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.052072 restraints weight = 18764.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.052451 restraints weight = 15811.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.9499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  10403  Z= 0.233
  Angle     :  0.780   7.831  15068  Z= 0.443
  Chirality :  0.048   0.301   1723
  Planarity :  0.006   0.055   1069
  Dihedral  : 33.026 176.365   3286
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 21.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.59 (0.33), residues: 578
  helix:  0.94 (0.23), residues: 464
  sheet:  None (None), residues: 0
  loop : -1.69 (0.47), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG B  35 
 TYR   0.022   0.002   TYR D  72 
 PHE   0.033   0.003   PHE G 104 
 HIS   0.006   0.002   HIS H  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00469 /  0.23 (10403)
  covalent geometry    : angle       0.78040 /  0.44 (15068)
  hydrogen bonds       : bond        0.06140 /  4.12 (  663)
  hydrogen bonds       : angle       3.56601 /  2.51 ( 1649)

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

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9425 (mtmt) cc_final: 0.9123 (mtmm)
REVERT: A   65 LEU cc_start: 0.9625 (tp) cc_final: 0.9376 (tp)
REVERT: A   85 GLN cc_start: 0.9374 (mt0) cc_final: 0.8731 (mt0)
REVERT: A   90 MET cc_start: 0.8140 (tmm) cc_final: 0.7936 (tmm)
REVERT: A  106 ASP cc_start: 0.9252 (t70) cc_final: 0.8866 (t70)
REVERT: A  133 GLU cc_start: 0.8554 (tt0) cc_final: 0.8220 (tt0)
REVERT: B   35 ARG cc_start: 0.8807 (ttm110) cc_final: 0.8521 (ttm110)
REVERT: B   74 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8143 (tm-30)
REVERT: B   85 ASP cc_start: 0.9299 (m-30) cc_final: 0.9022 (m-30)
REVERT: C   78 PHE cc_start: 0.8596 (t80) cc_final: 0.8226 (t80)
REVERT: C   90 MET cc_start: 0.9018 (ppp) cc_final: 0.8284 (ppp)
REVERT: C   93 GLN cc_start: 0.8863 (tm-30) cc_final: 0.8380 (tm-30)
REVERT: C   94 GLU cc_start: 0.9200 (pt0) cc_final: 0.8641 (pt0)
REVERT: C  123 ASP cc_start: 0.9442 (m-30) cc_final: 0.9235 (m-30)
REVERT: D   54 THR cc_start: 0.9461 (m) cc_final: 0.9157 (p)
REVERT: D   55 ARG cc_start: 0.9099 (mtt180) cc_final: 0.8496 (mmm-85)
REVERT: D   63 GLU cc_start: 0.9188 (tt0) cc_final: 0.8782 (tm-30)
REVERT: D   66 ILE cc_start: 0.9414 (mt) cc_final: 0.9212 (pt)
REVERT: E   64 LYS cc_start: 0.9140 (mmpt) cc_final: 0.8939 (mmmt)
REVERT: E   76 GLN cc_start: 0.9053 (tt0) cc_final: 0.8430 (tp-100)
REVERT: E   93 GLN cc_start: 0.9343 (mm110) cc_final: 0.8766 (tp40)
REVERT: E  106 ASP cc_start: 0.9121 (t0) cc_final: 0.8825 (t70)
REVERT: E  123 ASP cc_start: 0.9034 (m-30) cc_final: 0.8675 (m-30)
REVERT: F   49 LEU cc_start: 0.9304 (tp) cc_final: 0.9075 (tp)
REVERT: F   52 GLU cc_start: 0.8985 (mp0) cc_final: 0.8770 (mp0)
REVERT: F   55 ARG cc_start: 0.9181 (mtt90) cc_final: 0.8968 (mpt-90)
REVERT: F   60 VAL cc_start: 0.9006 (p) cc_final: 0.8488 (p)
REVERT: F   63 GLU cc_start: 0.9239 (pp20) cc_final: 0.8977 (pp20)
REVERT: F   64 ASN cc_start: 0.9002 (t0) cc_final: 0.8768 (t0)
REVERT: F   66 ILE cc_start: 0.9436 (mm) cc_final: 0.9166 (pt)
REVERT: G   90 MET cc_start: 0.8834 (ttm) cc_final: 0.8110 (tmm)
REVERT: G  128 ARG cc_start: 0.9013 (mtp-110) cc_final: 0.8165 (mtp-110)
REVERT: H   63 GLU cc_start: 0.8634 (tt0) cc_final: 0.8327 (tt0)
REVERT: H   95 ARG cc_start: 0.3652 (mpp-170) cc_final: 0.3412 (mpp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 258
  average time/residue: 0.1247
  time to fit residues: 42.3486
Evaluate side-chains
  219 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   chunk 37 optimal weight:    0.3980
   chunk 33 optimal weight:    5.9990
   chunk 75 optimal weight:   30.0000
   chunk 78 optimal weight:   40.0000
   chunk 1 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   overall best weight:    1.4384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  75 HIS
** G  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.065092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.050581 restraints weight = 57879.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.052014 restraints weight = 33814.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.052990 restraints weight = 23407.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.053602 restraints weight = 18086.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.054044 restraints weight = 15254.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.9516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072  10403  Z= 0.167
  Angle     :  0.751   9.766  15068  Z= 0.421
  Chirality :  0.047   0.315   1723
  Planarity :  0.006   0.070   1069
  Dihedral  : 32.942 175.351   3286
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 17.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.00 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.33), residues: 578
  helix:  1.14 (0.23), residues: 462
  sheet:  None (None), residues: 0
  loop : -1.65 (0.46), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG H  92 
 TYR   0.014   0.002   TYR D  72 
 PHE   0.026   0.002   PHE G 104 
 HIS   0.009   0.002   HIS D  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.17 (10403)
  covalent geometry    : angle       0.75108 /  0.42 (15068)
  hydrogen bonds       : bond        0.04660 /  3.10 (  663)
  hydrogen bonds       : angle       3.32719 /  2.35 ( 1649)

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

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 262
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 LEU cc_start: 0.9611 (tp) cc_final: 0.9355 (tp)
REVERT: A   85 GLN cc_start: 0.9372 (mt0) cc_final: 0.8722 (mt0)
REVERT: A   92 LEU cc_start: 0.9433 (mm) cc_final: 0.9230 (mm)
REVERT: A  106 ASP cc_start: 0.9191 (t70) cc_final: 0.8816 (t70)
REVERT: B   35 ARG cc_start: 0.8813 (ttm110) cc_final: 0.8554 (ttm110)
REVERT: B   85 ASP cc_start: 0.9204 (m-30) cc_final: 0.8980 (m-30)
REVERT: C   90 MET cc_start: 0.9001 (ppp) cc_final: 0.8275 (ppp)
REVERT: C   93 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8303 (tm-30)
REVERT: C   94 GLU cc_start: 0.9157 (pt0) cc_final: 0.8602 (pt0)
REVERT: D   54 THR cc_start: 0.9427 (m) cc_final: 0.9123 (p)
REVERT: D   55 ARG cc_start: 0.8952 (mtt180) cc_final: 0.8452 (mmm-85)
REVERT: D   63 GLU cc_start: 0.9200 (tt0) cc_final: 0.8801 (tm-30)
REVERT: D   66 ILE cc_start: 0.9395 (mt) cc_final: 0.9184 (pt)
REVERT: E   76 GLN cc_start: 0.9036 (tt0) cc_final: 0.8407 (tp-100)
REVERT: E  106 ASP cc_start: 0.9013 (t0) cc_final: 0.8741 (t70)
REVERT: E  123 ASP cc_start: 0.9004 (m-30) cc_final: 0.8616 (m-30)
REVERT: F   49 LEU cc_start: 0.9226 (tp) cc_final: 0.8962 (tp)
REVERT: F   52 GLU cc_start: 0.8932 (mp0) cc_final: 0.8689 (mp0)
REVERT: F   60 VAL cc_start: 0.8993 (p) cc_final: 0.8436 (p)
REVERT: F   63 GLU cc_start: 0.9228 (pp20) cc_final: 0.8971 (pp20)
REVERT: F   64 ASN cc_start: 0.8981 (t0) cc_final: 0.8749 (t0)
REVERT: F   66 ILE cc_start: 0.9427 (mm) cc_final: 0.9136 (pt)
REVERT: G   61 LEU cc_start: 0.8933 (tt) cc_final: 0.8432 (tt)
REVERT: G   90 MET cc_start: 0.8772 (ttm) cc_final: 0.8051 (tmm)
REVERT: G   97 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7746 (mt-10)
REVERT: G  106 ASP cc_start: 0.9195 (t70) cc_final: 0.8961 (t70)
REVERT: G  123 ASP cc_start: 0.9127 (m-30) cc_final: 0.8855 (m-30)
REVERT: G  128 ARG cc_start: 0.9021 (mtp-110) cc_final: 0.8264 (mtp-110)
REVERT: H   74 GLU cc_start: 0.9037 (tt0) cc_final: 0.8516 (tt0)
REVERT: H   95 ARG cc_start: 0.3622 (mpp-170) cc_final: 0.3363 (mpp-170)
  outliers start: 1
  outliers final: 1
  residues processed: 262
  average time/residue: 0.1196
  time to fit residues: 41.8629
Evaluate side-chains
  230 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 229
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 16 optimal weight:    0.0030
   chunk 39 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 56 optimal weight:   50.0000
   chunk 10 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 77 optimal weight:   30.0000
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.9796

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.065901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.051084 restraints weight = 58974.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.052481 restraints weight = 35460.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.053438 restraints weight = 25039.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.054066 restraints weight = 19625.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.054471 restraints weight = 16621.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.9559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  10403  Z= 0.161
  Angle     :  0.732   8.058  15068  Z= 0.412
  Chirality :  0.046   0.313   1723
  Planarity :  0.006   0.062   1069
  Dihedral  : 32.791 175.595   3286
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.34), residues: 578
  helix:  1.17 (0.24), residues: 457
  sheet:  None (None), residues: 0
  loop : -1.74 (0.47), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG H  35 
 TYR   0.012   0.002   TYR D  72 
 PHE   0.020   0.002   PHE A 104 
 HIS   0.005   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.16 (10403)
  covalent geometry    : angle       0.73208 /  0.41 (15068)
  hydrogen bonds       : bond        0.04529 /  3.03 (  663)
  hydrogen bonds       : angle       3.30840 /  2.34 ( 1649)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1694.77 seconds
wall clock time: 30 minutes 4.20 seconds (1804.20 seconds total)