Starting phenix.real_space_refine
on Thu Feb 13 21:03:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yoz_33991/02_2025/7yoz_33991.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yoz_33991/02_2025/7yoz_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_33991/02_2025/7yoz_33991.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yoz_33991/02_2025/7yoz_33991.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yoz_33991/02_2025/7yoz_33991.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yoz_33991/02_2025/7yoz_33991.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.75, per 1000 atoms: 0.59
  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: 2.32
  Conformation dependent library (CDL) restraints added in 605.6 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: 4.50
  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: 3.31

  Time building geometry restraints manager: 2.73 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=" O3'  DT I  14 "
    ideal  model  delta    sigma   weight residual
    1.422  1.459 -0.037 3.00e-02 1.11e+03 1.52e+00
  bond pdb=" CB  ARG G 128 "
       pdb=" CG  ARG G 128 "
    ideal  model  delta    sigma   weight residual
    1.520  1.556 -0.036 3.00e-02 1.11e+03 1.41e+00
  bond pdb=" CD  ARG A 131 "
       pdb=" NE  ARG A 131 "
    ideal  model  delta    sigma   weight residual
    1.458  1.474 -0.016 1.40e-02 5.10e+03 1.37e+00
  bond pdb=" CG  ARG B  92 "
       pdb=" CD  ARG B  92 "
    ideal  model  delta    sigma   weight residual
    1.520  1.487  0.033 3.00e-02 1.11e+03 1.20e+00
  bond pdb=" CE  LYS G  64 "
       pdb=" NZ  LYS G  64 "
    ideal  model  delta    sigma   weight residual
    1.489  1.457  0.032 3.00e-02 1.11e+03 1.15e+00
  ... (remaining 10398 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 14709
        1.58 -     3.17: 337
        3.17 -     4.75: 13
        4.75 -     6.33: 6
        6.33 -     7.92: 3
  Bond angle restraints: 15068
  Sorted by residual:
  angle pdb=" CB  LEU A 103 "
        pdb=" CG  LEU A 103 "
        pdb=" CD1 LEU A 103 "
      ideal   model   delta    sigma   weight residual
     110.70  103.05    7.65 3.00e+00 1.11e-01 6.50e+00
  angle pdb=" N   SER C  86 "
        pdb=" CA  SER C  86 "
        pdb=" C   SER C  86 "
      ideal   model   delta    sigma   weight residual
     111.07  113.75   -2.68 1.07e+00 8.73e-01 6.25e+00
  angle pdb=" CA  LEU B  62 "
        pdb=" CB  LEU B  62 "
        pdb=" CG  LEU B  62 "
      ideal   model   delta    sigma   weight residual
     116.30  124.22   -7.92 3.50e+00 8.16e-02 5.12e+00
  angle pdb=" NE  ARG B  92 "
        pdb=" CZ  ARG B  92 "
        pdb=" NH1 ARG B  92 "
      ideal   model   delta    sigma   weight residual
     121.50  119.26    2.24 1.00e+00 1.00e+00 5.00e+00
  angle pdb=" C   LEU B  90 "
        pdb=" N   LYS B  91 "
        pdb=" CA  LYS B  91 "
      ideal   model   delta    sigma   weight residual
     120.28  123.27   -2.99 1.34e+00 5.57e-01 4.97e+00
  ... (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: 1559
       0.050 -    0.101: 141
       0.101 -    0.151: 20
       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:             0.320
  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:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     26.610
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10403  Z= 0.171
  Angle     :  0.552   7.918  15068  Z= 0.361
  Chirality :  0.032   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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (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
 HIS   0.005   0.001   HIS A 113 
 PHE   0.014   0.001   PHE G 104 
 TYR   0.012   0.001   TYR D  88 
 ARG   0.024   0.001   ARG B  92 

*********************** 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  : 0.682 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.8892 (mttm) cc_final: 0.8550 (mtmm)
REVERT: A   68 GLN cc_start: 0.8865 (tt0) cc_final: 0.8408 (tp40)
REVERT: A   85 GLN cc_start: 0.8636 (tt0) cc_final: 0.8300 (tp40)
REVERT: A   93 GLN cc_start: 0.8676 (tt0) cc_final: 0.8038 (tm-30)
REVERT: A  119 ILE cc_start: 0.9037 (pt) cc_final: 0.8346 (mt)
REVERT: A  120 MET cc_start: 0.8634 (mmm) cc_final: 0.8410 (mmm)
REVERT: A  123 ASP cc_start: 0.8834 (m-30) cc_final: 0.8472 (t70)
REVERT: A  126 LEU cc_start: 0.9647 (tp) cc_final: 0.9430 (tp)
REVERT: A  128 ARG cc_start: 0.8893 (mtp180) cc_final: 0.8313 (mtp180)
REVERT: A  130 ILE cc_start: 0.9707 (mt) cc_final: 0.9487 (mm)
REVERT: B   51 TYR cc_start: 0.8033 (m-80) cc_final: 0.7735 (m-80)
REVERT: C  104 PHE cc_start: 0.9000 (m-80) cc_final: 0.8537 (m-80)
REVERT: C  121 PRO cc_start: 0.8849 (Cg_exo) cc_final: 0.8627 (Cg_endo)
REVERT: C  123 ASP cc_start: 0.8886 (m-30) cc_final: 0.8366 (m-30)
REVERT: C  124 ILE cc_start: 0.9349 (mt) cc_final: 0.9097 (tp)
REVERT: C  130 ILE cc_start: 0.8366 (tt) cc_final: 0.8042 (tt)
REVERT: D   43 VAL cc_start: 0.8313 (t) cc_final: 0.7889 (t)
REVERT: D   52 GLU cc_start: 0.9122 (tt0) cc_final: 0.8831 (pp20)
REVERT: D   55 ARG cc_start: 0.8771 (mtt180) cc_final: 0.8372 (mmm-85)
REVERT: D   59 LYS cc_start: 0.9150 (tttt) cc_final: 0.8326 (tptt)
REVERT: D   66 ILE cc_start: 0.9140 (mm) cc_final: 0.8911 (pt)
REVERT: D   71 THR cc_start: 0.8948 (m) cc_final: 0.8443 (m)
REVERT: E   60 LEU cc_start: 0.6207 (mt) cc_final: 0.5995 (mp)
REVERT: E   70 LEU cc_start: 0.8786 (tp) cc_final: 0.8246 (tt)
REVERT: E   87 SER cc_start: 0.8980 (m) cc_final: 0.8511 (p)
REVERT: E  104 PHE cc_start: 0.8998 (m-80) cc_final: 0.8464 (m-80)
REVERT: E  109 LEU cc_start: 0.9725 (tp) cc_final: 0.9503 (tp)
REVERT: E  126 LEU cc_start: 0.9139 (tp) cc_final: 0.8919 (tt)
REVERT: F   59 LYS cc_start: 0.9204 (tttt) cc_final: 0.8908 (ttpt)
REVERT: F   66 ILE cc_start: 0.9055 (mm) cc_final: 0.8817 (pt)
REVERT: G   70 LEU cc_start: 0.9140 (tp) cc_final: 0.8380 (tt)
REVERT: G   90 MET cc_start: 0.8385 (ttm) cc_final: 0.8051 (tmm)
REVERT: G   97 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7721 (mt-10)
REVERT: G  123 ASP cc_start: 0.8589 (m-30) cc_final: 0.8368 (t70)
REVERT: H   35 ARG cc_start: 0.8395 (mtp85) cc_final: 0.7964 (ttt180)
REVERT: H   43 VAL cc_start: 0.6861 (t) cc_final: 0.5771 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 335
  average time/residue: 0.3710
  time to fit residues: 153.0931
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  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:   10.0000
   chunk 60 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 62 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 72 optimal weight:   10.0000
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
G  68 GLN
** H  75 HIS ** 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 = 0.3907 r_free = 0.3907 target = 0.088028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.073697 restraints weight = 54351.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.075282 restraints weight = 33788.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.076407 restraints weight = 23880.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.4117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10403  Z= 0.230
  Angle     :  0.622   6.563  15068  Z= 0.363
  Chirality :  0.035   0.144   1723
  Planarity :  0.005   0.086   1069
  Dihedral  : 31.296 179.525   3286
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 15.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  4.56 %
    Favored  : 94.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.33), residues: 578
  helix:  1.92 (0.23), residues: 468
  sheet:  None (None), residues: 0
  loop : -1.07 (0.49), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.003   HIS F  75 
 PHE   0.015   0.002   PHE A 104 
 TYR   0.019   0.002   TYR D  72 
 ARG   0.010   0.001   ARG E  69 

*********************** 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
  262 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 259
  time to evaluate  : 0.631 
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: 0.7807 (tt) cc_final: 0.7493 (tt)
REVERT: A   64 LYS cc_start: 0.9359 (mttm) cc_final: 0.8804 (mtmm)
REVERT: A   68 GLN cc_start: 0.9173 (tt0) cc_final: 0.8942 (tp-100)
REVERT: A   85 GLN cc_start: 0.9093 (tt0) cc_final: 0.8567 (tp40)
REVERT: A   93 GLN cc_start: 0.9014 (tt0) cc_final: 0.8112 (tm-30)
REVERT: A   96 CYS cc_start: 0.9073 (m) cc_final: 0.8724 (m)
REVERT: A  107 THR cc_start: 0.8953 (p) cc_final: 0.8749 (p)
REVERT: A  119 ILE cc_start: 0.9114 (pt) cc_final: 0.8811 (mt)
REVERT: A  123 ASP cc_start: 0.8843 (m-30) cc_final: 0.8368 (t70)
REVERT: A  130 ILE cc_start: 0.9759 (mt) cc_final: 0.9506 (mm)
REVERT: B   24 ASP cc_start: 0.8156 (t0) cc_final: 0.7427 (p0)
REVERT: C   90 MET cc_start: 0.9199 (ppp) cc_final: 0.8746 (ppp)
REVERT: C   93 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8837 (tm-30)
REVERT: C   94 GLU cc_start: 0.9247 (pt0) cc_final: 0.8900 (pt0)
REVERT: C  100 LEU cc_start: 0.9452 (tp) cc_final: 0.9104 (tp)
REVERT: C  104 PHE cc_start: 0.9032 (m-80) cc_final: 0.8457 (m-80)
REVERT: C  106 ASP cc_start: 0.9108 (m-30) cc_final: 0.8547 (m-30)
REVERT: C  129 ARG cc_start: 0.8307 (tpm170) cc_final: 0.7776 (tpm170)
REVERT: D   49 LEU cc_start: 0.8294 (pp) cc_final: 0.7956 (pt)
REVERT: D   55 ARG cc_start: 0.8922 (mtt180) cc_final: 0.8454 (mmm-85)
REVERT: D   59 LYS cc_start: 0.9124 (tttt) cc_final: 0.8354 (tptp)
REVERT: D   66 ILE cc_start: 0.9068 (mm) cc_final: 0.8819 (pt)
REVERT: E   87 SER cc_start: 0.8883 (m) cc_final: 0.8462 (p)
REVERT: E   93 GLN cc_start: 0.9307 (mm110) cc_final: 0.8973 (tp40)
REVERT: E  120 MET cc_start: 0.8631 (mmp) cc_final: 0.8159 (mmm)
REVERT: E  123 ASP cc_start: 0.9072 (m-30) cc_final: 0.8830 (m-30)
REVERT: E  128 ARG cc_start: 0.8970 (mmm-85) cc_final: 0.8384 (mmm-85)
REVERT: E  129 ARG cc_start: 0.8642 (tmt-80) cc_final: 0.8224 (tpm170)
REVERT: F   63 GLU cc_start: 0.8808 (tt0) cc_final: 0.8341 (tm-30)
REVERT: F   66 ILE cc_start: 0.9054 (mm) cc_final: 0.8851 (pt)
REVERT: G   68 GLN cc_start: 0.9012 (tm130) cc_final: 0.8529 (tm-30)
REVERT: G   90 MET cc_start: 0.8626 (ttm) cc_final: 0.8239 (tmm)
REVERT: G   96 CYS cc_start: 0.8177 (m) cc_final: 0.7810 (m)
REVERT: G   97 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7889 (mt-10)
REVERT: G  123 ASP cc_start: 0.8774 (m-30) cc_final: 0.8352 (t70)
REVERT: G  128 ARG cc_start: 0.9178 (mtp-110) cc_final: 0.8965 (mtp-110)
REVERT: H   46 ILE cc_start: 0.8784 (mp) cc_final: 0.8528 (mt)
REVERT: H   74 GLU cc_start: 0.9114 (tt0) cc_final: 0.8669 (tt0)
  outliers start: 3
  outliers final: 0
  residues processed: 262
  average time/residue: 0.3161
  time to fit residues: 103.5794
Evaluate side-chains
  206 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 76 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   chunk 72 optimal weight:   10.0000
   chunk 70 optimal weight:   10.0000
   chunk 71 optimal weight:    8.9990
   chunk 61 optimal weight:   10.0000
   chunk 63 optimal weight:    8.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  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 = 0.3587 r_free = 0.3587 target = 0.070025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.055701 restraints weight = 57937.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.057119 restraints weight = 34206.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.058098 restraints weight = 23874.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.7607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  10403  Z= 0.334
  Angle     :  0.717   6.401  15068  Z= 0.418
  Chirality :  0.038   0.266   1723
  Planarity :  0.006   0.052   1069
  Dihedral  : 32.167 179.024   3286
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 17.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  5.75 %
    Favored  : 93.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.33), residues: 578
  helix:  1.51 (0.23), residues: 454
  sheet:  None (None), residues: 0
  loop : -1.02 (0.45), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.003   HIS A 113 
 PHE   0.018   0.002   PHE A 104 
 TYR   0.014   0.002   TYR B  88 
 ARG   0.010   0.001   ARG D  36 

*********************** 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
  283 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 281
  time to evaluate  : 0.767 
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   60 LEU cc_start: 0.8945 (mm) cc_final: 0.8463 (mt)
REVERT: A   61 LEU cc_start: 0.8939 (tt) cc_final: 0.8660 (tp)
REVERT: A   64 LYS cc_start: 0.9560 (mttm) cc_final: 0.9230 (mtmm)
REVERT: A   68 GLN cc_start: 0.9342 (tt0) cc_final: 0.8990 (tt0)
REVERT: A   73 GLU cc_start: 0.9026 (pp20) cc_final: 0.8487 (pp20)
REVERT: A   76 GLN cc_start: 0.8566 (tp-100) cc_final: 0.8127 (tm-30)
REVERT: A   93 GLN cc_start: 0.9261 (tt0) cc_final: 0.7650 (tm-30)
REVERT: A   94 GLU cc_start: 0.8976 (pt0) cc_final: 0.8385 (pt0)
REVERT: A   96 CYS cc_start: 0.8702 (m) cc_final: 0.8257 (m)
REVERT: A   97 GLU cc_start: 0.8287 (mt-10) cc_final: 0.6886 (mt-10)
REVERT: A  109 LEU cc_start: 0.9339 (tt) cc_final: 0.9104 (tt)
REVERT: A  120 MET cc_start: 0.8995 (mmm) cc_final: 0.8450 (mmm)
REVERT: A  130 ILE cc_start: 0.9770 (mt) cc_final: 0.9517 (mt)
REVERT: B   24 ASP cc_start: 0.8626 (t0) cc_final: 0.7739 (p0)
REVERT: B   52 GLU cc_start: 0.9020 (tp30) cc_final: 0.8802 (tp30)
REVERT: B   63 GLU cc_start: 0.8738 (tt0) cc_final: 0.8084 (tp30)
REVERT: B   74 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8131 (tm-30)
REVERT: B   85 ASP cc_start: 0.9398 (m-30) cc_final: 0.9090 (m-30)
REVERT: B   88 TYR cc_start: 0.8867 (m-10) cc_final: 0.8667 (m-10)
REVERT: B   92 ARG cc_start: 0.8099 (ttt180) cc_final: 0.7898 (tmm-80)
REVERT: C   78 PHE cc_start: 0.8376 (t80) cc_final: 0.8025 (t80)
REVERT: C   90 MET cc_start: 0.9173 (ppp) cc_final: 0.8570 (ppp)
REVERT: C   93 GLN cc_start: 0.9148 (tm-30) cc_final: 0.8686 (tm-30)
REVERT: C  106 ASP cc_start: 0.9162 (m-30) cc_final: 0.8646 (m-30)
REVERT: C  129 ARG cc_start: 0.8679 (tpm170) cc_final: 0.8266 (tpm170)
REVERT: D   55 ARG cc_start: 0.9123 (mtt180) cc_final: 0.8544 (mmm-85)
REVERT: D   59 LYS cc_start: 0.9380 (tttt) cc_final: 0.8636 (tptp)
REVERT: D   63 GLU cc_start: 0.9148 (tt0) cc_final: 0.8751 (tm-30)
REVERT: E   76 GLN cc_start: 0.8831 (tt0) cc_final: 0.8263 (tp-100)
REVERT: E   90 MET cc_start: 0.8674 (ppp) cc_final: 0.8236 (ppp)
REVERT: E   93 GLN cc_start: 0.9325 (mm110) cc_final: 0.9039 (mm110)
REVERT: E  119 ILE cc_start: 0.8670 (pt) cc_final: 0.8251 (pt)
REVERT: E  120 MET cc_start: 0.8752 (mmp) cc_final: 0.8389 (mmm)
REVERT: F   55 ARG cc_start: 0.8737 (mmm-85) cc_final: 0.8128 (mmm-85)
REVERT: F   84 MET cc_start: 0.8755 (ptt) cc_final: 0.8471 (ptt)
REVERT: F   88 TYR cc_start: 0.9102 (m-80) cc_final: 0.8689 (t80)
REVERT: G   60 LEU cc_start: 0.8640 (mm) cc_final: 0.8158 (mm)
REVERT: G   73 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8801 (tm-30)
REVERT: G   90 MET cc_start: 0.8825 (ttm) cc_final: 0.8296 (tmm)
REVERT: G   93 GLN cc_start: 0.8966 (pt0) cc_final: 0.8204 (pt0)
REVERT: G   94 GLU cc_start: 0.8760 (pt0) cc_final: 0.8533 (pt0)
REVERT: G   97 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7678 (mt-10)
REVERT: G  123 ASP cc_start: 0.8887 (m-30) cc_final: 0.8606 (t70)
REVERT: H   35 ARG cc_start: 0.8353 (mmt180) cc_final: 0.8125 (mmt180)
REVERT: H   39 ARG cc_start: 0.8856 (mmt90) cc_final: 0.8624 (mmt90)
REVERT: H   67 ARG cc_start: 0.9244 (ttm170) cc_final: 0.8960 (ttm170)
REVERT: H   68 ASP cc_start: 0.9283 (m-30) cc_final: 0.9075 (m-30)
REVERT: H   74 GLU cc_start: 0.9149 (tt0) cc_final: 0.8786 (tt0)
REVERT: H   88 TYR cc_start: 0.8591 (m-10) cc_final: 0.8231 (m-10)
  outliers start: 2
  outliers final: 1
  residues processed: 282
  average time/residue: 0.3086
  time to fit residues: 109.7610
Evaluate side-chains
  231 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 230
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 56 optimal weight:   20.0000
   chunk 73 optimal weight:   10.0000
   chunk 51 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 26 optimal weight:    6.9990
   chunk 71 optimal weight:    8.9990
   chunk 25 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   chunk 33 optimal weight:   10.0000
   overall best weight:    4.1788

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

Flipped N/Q/H residues before XYZ refinement:
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 113 HIS
** G 108 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 = 0.3481 r_free = 0.3481 target = 0.064545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.050036 restraints weight = 59526.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.051369 restraints weight = 35397.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.052284 restraints weight = 25033.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.9437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  10403  Z= 0.309
  Angle     :  0.691   8.089  15068  Z= 0.409
  Chirality :  0.037   0.174   1723
  Planarity :  0.006   0.057   1069
  Dihedral  : 32.522 178.996   3286
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 17.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  4.76 %
    Favored  : 95.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.33), residues: 578
  helix:  1.42 (0.23), residues: 454
  sheet:  None (None), residues: 0
  loop : -0.87 (0.45), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.003   HIS A 113 
 PHE   0.020   0.002   PHE G 104 
 TYR   0.011   0.002   TYR F  51 
 ARG   0.013   0.001   ARG A  72 

*********************** 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
  281 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 280
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 LEU cc_start: 0.9558 (tp) cc_final: 0.9348 (tp)
REVERT: A   85 GLN cc_start: 0.9206 (tt0) cc_final: 0.8850 (tp40)
REVERT: A   90 MET cc_start: 0.8277 (tmm) cc_final: 0.7957 (tmm)
REVERT: A  106 ASP cc_start: 0.9029 (t70) cc_final: 0.8766 (t70)
REVERT: A  107 THR cc_start: 0.9707 (p) cc_final: 0.9194 (p)
REVERT: A  115 LYS cc_start: 0.9077 (mmmt) cc_final: 0.8725 (mmmm)
REVERT: A  123 ASP cc_start: 0.8856 (m-30) cc_final: 0.8517 (t70)
REVERT: B   24 ASP cc_start: 0.8592 (t0) cc_final: 0.8058 (p0)
REVERT: B   31 LYS cc_start: 0.9328 (mttp) cc_final: 0.9107 (mtpp)
REVERT: B   63 GLU cc_start: 0.8758 (tt0) cc_final: 0.8545 (tt0)
REVERT: B   74 GLU cc_start: 0.8512 (tm-30) cc_final: 0.7962 (tm-30)
REVERT: B   85 ASP cc_start: 0.9345 (m-30) cc_final: 0.9117 (m-30)
REVERT: C   90 MET cc_start: 0.9036 (ppp) cc_final: 0.8325 (ppp)
REVERT: C   94 GLU cc_start: 0.9262 (pt0) cc_final: 0.8644 (pt0)
REVERT: C  106 ASP cc_start: 0.8858 (m-30) cc_final: 0.8228 (m-30)
REVERT: D   55 ARG cc_start: 0.9092 (mtt180) cc_final: 0.8493 (mmm-85)
REVERT: D   63 GLU cc_start: 0.9246 (tt0) cc_final: 0.8756 (tm-30)
REVERT: E   64 LYS cc_start: 0.9096 (mmmt) cc_final: 0.8663 (mmmm)
REVERT: E   76 GLN cc_start: 0.9005 (tt0) cc_final: 0.8416 (tp-100)
REVERT: E  110 CYS cc_start: 0.8716 (t) cc_final: 0.8276 (t)
REVERT: E  119 ILE cc_start: 0.8883 (pt) cc_final: 0.8522 (pt)
REVERT: E  123 ASP cc_start: 0.9099 (m-30) cc_final: 0.8694 (m-30)
REVERT: F   63 GLU cc_start: 0.9375 (tt0) cc_final: 0.9082 (tm-30)
REVERT: F   78 ARG cc_start: 0.7011 (ptm160) cc_final: 0.6782 (ptm160)
REVERT: F   82 THR cc_start: 0.8121 (p) cc_final: 0.7759 (p)
REVERT: F   84 MET cc_start: 0.8857 (ptt) cc_final: 0.8601 (ptt)
REVERT: G   60 LEU cc_start: 0.8674 (mm) cc_final: 0.8359 (mt)
REVERT: G   61 LEU cc_start: 0.9160 (tt) cc_final: 0.8578 (tt)
REVERT: G   68 GLN cc_start: 0.9171 (pp30) cc_final: 0.8953 (pp30)
REVERT: G   90 MET cc_start: 0.8786 (ttm) cc_final: 0.8204 (tmm)
REVERT: G   93 GLN cc_start: 0.8890 (pt0) cc_final: 0.7965 (pt0)
REVERT: G   94 GLU cc_start: 0.8873 (pt0) cc_final: 0.8646 (pt0)
REVERT: G   97 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7822 (mt-10)
REVERT: G  107 THR cc_start: 0.9685 (p) cc_final: 0.9409 (p)
REVERT: G  123 ASP cc_start: 0.8774 (m-30) cc_final: 0.8485 (t70)
REVERT: G  128 ARG cc_start: 0.9029 (mtp-110) cc_final: 0.8320 (mtp-110)
REVERT: H   52 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8643 (tp30)
REVERT: H   65 VAL cc_start: 0.9589 (t) cc_final: 0.9388 (p)
REVERT: H   74 GLU cc_start: 0.9098 (tt0) cc_final: 0.8770 (tt0)
REVERT: H   88 TYR cc_start: 0.8667 (m-10) cc_final: 0.8093 (m-10)
REVERT: H   95 ARG cc_start: 0.3510 (mpp-170) cc_final: 0.3296 (mpp-170)
  outliers start: 1
  outliers final: 1
  residues processed: 280
  average time/residue: 0.3019
  time to fit residues: 107.1277
Evaluate side-chains
  234 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 233
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 11 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9990
   chunk 60 optimal weight:   10.0000
   chunk 56 optimal weight:   20.0000
   chunk 78 optimal weight:   10.0000
   chunk 76 optimal weight:    7.9990
   chunk 36 optimal weight:    6.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    4.1788

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A  93 GLN
** C  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  75 HIS
F  27 GLN
** H  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.061790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.047352 restraints weight = 58844.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.048608 restraints weight = 35965.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.049503 restraints weight = 25912.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          1.0399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044  10403  Z= 0.315
  Angle     :  0.705  11.332  15068  Z= 0.414
  Chirality :  0.037   0.208   1723
  Planarity :  0.005   0.050   1069
  Dihedral  : 32.795 179.598   3286
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 19.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.33), residues: 578
  helix:  1.29 (0.23), residues: 457
  sheet:  None (None), residues: 0
  loop : -1.14 (0.45), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.003   HIS D  75 
 PHE   0.019   0.002   PHE G 104 
 TYR   0.011   0.002   TYR B  51 
 ARG   0.008   0.001   ARG H  92 

*********************** 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
  278 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 278
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9396 (mtmt) cc_final: 0.9049 (mtmm)
REVERT: A   68 GLN cc_start: 0.9544 (tt0) cc_final: 0.9340 (tt0)
REVERT: A   73 GLU cc_start: 0.9064 (pp20) cc_final: 0.8749 (pp20)
REVERT: A   90 MET cc_start: 0.8295 (tmm) cc_final: 0.8019 (tmm)
REVERT: A  105 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8299 (tm-30)
REVERT: A  106 ASP cc_start: 0.9137 (t70) cc_final: 0.8416 (t70)
REVERT: A  115 LYS cc_start: 0.9113 (mmmt) cc_final: 0.8784 (mmmm)
REVERT: B   24 ASP cc_start: 0.8672 (t0) cc_final: 0.7782 (t0)
REVERT: B   31 LYS cc_start: 0.9444 (mttp) cc_final: 0.9230 (mtpp)
REVERT: B   63 GLU cc_start: 0.8741 (tt0) cc_final: 0.8323 (tp30)
REVERT: B   74 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8018 (tm-30)
REVERT: B   85 ASP cc_start: 0.9375 (m-30) cc_final: 0.9150 (m-30)
REVERT: C   78 PHE cc_start: 0.8617 (t80) cc_final: 0.8278 (t80)
REVERT: C   90 MET cc_start: 0.9021 (ppp) cc_final: 0.8556 (ppp)
REVERT: C   93 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7825 (tm-30)
REVERT: C   94 GLU cc_start: 0.9202 (pt0) cc_final: 0.8987 (pt0)
REVERT: C  123 ASP cc_start: 0.9331 (m-30) cc_final: 0.9093 (m-30)
REVERT: D   55 ARG cc_start: 0.9042 (mtt180) cc_final: 0.8384 (mmm-85)
REVERT: D   63 GLU cc_start: 0.9071 (tt0) cc_final: 0.8815 (tm-30)
REVERT: E   76 GLN cc_start: 0.9042 (tt0) cc_final: 0.8462 (tp-100)
REVERT: E  110 CYS cc_start: 0.8595 (t) cc_final: 0.8124 (t)
REVERT: E  123 ASP cc_start: 0.9010 (m-30) cc_final: 0.8479 (m-30)
REVERT: F   29 ILE cc_start: 0.9628 (mm) cc_final: 0.9385 (mm)
REVERT: F   63 GLU cc_start: 0.9384 (tt0) cc_final: 0.8980 (tm-30)
REVERT: F   82 THR cc_start: 0.8033 (p) cc_final: 0.7797 (p)
REVERT: G   60 LEU cc_start: 0.8726 (mm) cc_final: 0.8509 (mt)
REVERT: G   61 LEU cc_start: 0.9213 (tt) cc_final: 0.8825 (tt)
REVERT: G   73 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8759 (tm-30)
REVERT: G   93 GLN cc_start: 0.8642 (pt0) cc_final: 0.7836 (pt0)
REVERT: G   94 GLU cc_start: 0.9020 (pt0) cc_final: 0.8654 (pt0)
REVERT: G   97 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8132 (mt-10)
REVERT: G  107 THR cc_start: 0.9699 (p) cc_final: 0.9388 (p)
REVERT: G  123 ASP cc_start: 0.8869 (m-30) cc_final: 0.8452 (t70)
REVERT: G  125 GLN cc_start: 0.9212 (mm-40) cc_final: 0.8904 (tp40)
REVERT: G  128 ARG cc_start: 0.8947 (mtp-110) cc_final: 0.8133 (mtp-110)
REVERT: H   39 ARG cc_start: 0.8734 (mmt90) cc_final: 0.8386 (mmt90)
REVERT: H   74 GLU cc_start: 0.9072 (tt0) cc_final: 0.8728 (tt0)
REVERT: H   88 TYR cc_start: 0.8773 (m-10) cc_final: 0.8202 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 278
  average time/residue: 0.2914
  time to fit residues: 103.7036
Evaluate side-chains
  238 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 68 optimal weight:   20.0000
   chunk 59 optimal weight:    9.9990
   chunk 79 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 14 optimal weight:   10.9990
   chunk 57 optimal weight:   10.0000
   chunk 55 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
** 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 = 0.3469 r_free = 0.3469 target = 0.063708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.049239 restraints weight = 59522.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.050629 restraints weight = 34635.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.051551 restraints weight = 24106.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          1.0575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10403  Z= 0.226
  Angle     :  0.678  11.846  15068  Z= 0.390
  Chirality :  0.036   0.179   1723
  Planarity :  0.004   0.034   1069
  Dihedral  : 32.589 179.306   3286
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 15.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.33), residues: 578
  helix:  1.31 (0.23), residues: 460
  sheet:  None (None), residues: 0
  loop : -1.21 (0.48), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS A 113 
 PHE   0.020   0.002   PHE G 104 
 TYR   0.017   0.001   TYR D  72 
 ARG   0.009   0.001   ARG H  92 

*********************** 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
  288 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 288
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9306 (mtmt) cc_final: 0.8969 (mtmm)
REVERT: A   65 LEU cc_start: 0.9634 (tp) cc_final: 0.9426 (tp)
REVERT: A   90 MET cc_start: 0.8231 (tmm) cc_final: 0.7994 (tmm)
REVERT: A  106 ASP cc_start: 0.9194 (t70) cc_final: 0.8631 (t70)
REVERT: A  115 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8687 (mmmm)
REVERT: B   24 ASP cc_start: 0.8680 (t0) cc_final: 0.8290 (p0)
REVERT: B   31 LYS cc_start: 0.9420 (mttp) cc_final: 0.9191 (mtpp)
REVERT: B   43 VAL cc_start: 0.8589 (t) cc_final: 0.8279 (t)
REVERT: B   74 GLU cc_start: 0.8538 (tm-30) cc_final: 0.7771 (tm-30)
REVERT: C   90 MET cc_start: 0.8987 (ppp) cc_final: 0.8505 (ppp)
REVERT: C  123 ASP cc_start: 0.9377 (m-30) cc_final: 0.9103 (m-30)
REVERT: D   55 ARG cc_start: 0.9026 (mtt180) cc_final: 0.8236 (mmm-85)
REVERT: D   63 GLU cc_start: 0.9082 (tt0) cc_final: 0.8823 (tm-30)
REVERT: E   64 LYS cc_start: 0.8741 (mmmt) cc_final: 0.8398 (mmmm)
REVERT: E   76 GLN cc_start: 0.9025 (tt0) cc_final: 0.8487 (tp-100)
REVERT: E  103 LEU cc_start: 0.9160 (tt) cc_final: 0.8775 (pp)
REVERT: E  105 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8079 (mm-30)
REVERT: E  110 CYS cc_start: 0.8514 (t) cc_final: 0.7895 (t)
REVERT: E  123 ASP cc_start: 0.9024 (m-30) cc_final: 0.8523 (m-30)
REVERT: E  134 ARG cc_start: 0.8076 (mmp80) cc_final: 0.7789 (mmm160)
REVERT: F   27 GLN cc_start: 0.9045 (mm110) cc_final: 0.8844 (mm-40)
REVERT: F   29 ILE cc_start: 0.9562 (mm) cc_final: 0.9301 (mm)
REVERT: F   63 GLU cc_start: 0.9463 (tt0) cc_final: 0.8980 (tm-30)
REVERT: F   67 ARG cc_start: 0.9334 (ttp80) cc_final: 0.9065 (ttp80)
REVERT: F   78 ARG cc_start: 0.7450 (ptm160) cc_final: 0.6904 (ptm160)
REVERT: F   79 LYS cc_start: 0.8618 (mmmt) cc_final: 0.8302 (mmmm)
REVERT: F   82 THR cc_start: 0.8008 (p) cc_final: 0.7469 (p)
REVERT: G   61 LEU cc_start: 0.9068 (tt) cc_final: 0.8703 (tt)
REVERT: G   83 ARG cc_start: 0.8169 (mtp-110) cc_final: 0.7863 (mmm-85)
REVERT: G   93 GLN cc_start: 0.8622 (pt0) cc_final: 0.7899 (pt0)
REVERT: G   94 GLU cc_start: 0.8890 (pt0) cc_final: 0.8633 (pt0)
REVERT: G   97 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8117 (mt-10)
REVERT: G  120 MET cc_start: 0.8765 (mmm) cc_final: 0.8540 (mmm)
REVERT: G  123 ASP cc_start: 0.8903 (m-30) cc_final: 0.8595 (m-30)
REVERT: G  125 GLN cc_start: 0.9195 (mm-40) cc_final: 0.8854 (tp40)
REVERT: G  128 ARG cc_start: 0.8937 (mtp-110) cc_final: 0.8154 (mtp-110)
REVERT: H   35 ARG cc_start: 0.8364 (mmt180) cc_final: 0.7993 (tpt170)
REVERT: H   88 TYR cc_start: 0.8630 (m-10) cc_final: 0.8068 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 288
  average time/residue: 0.2822
  time to fit residues: 104.5660
Evaluate side-chains
  245 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 70 optimal weight:   10.0000
   chunk 59 optimal weight:   10.0000
   chunk 8 optimal weight:    8.9990
   chunk 28 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 31 optimal weight:    9.9990
   chunk 27 optimal weight:    8.9990
   chunk 54 optimal weight:    7.9990
   chunk 35 optimal weight:    2.9990
   chunk 67 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A  93 GLN
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
H  25 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.057921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.043518 restraints weight = 60643.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.044805 restraints weight = 35386.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.045670 restraints weight = 24840.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          1.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068  10403  Z= 0.390
  Angle     :  0.764  10.347  15068  Z= 0.447
  Chirality :  0.040   0.156   1723
  Planarity :  0.006   0.046   1069
  Dihedral  : 33.179 178.884   3286
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 21.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  2.38 %
    Favored  : 97.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.33), residues: 578
  helix:  1.04 (0.23), residues: 461
  sheet:  None (None), residues: 0
  loop : -1.42 (0.49), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.002   HIS A 113 
 PHE   0.030   0.003   PHE G 104 
 TYR   0.025   0.003   TYR F  51 
 ARG   0.026   0.001   ARG F  35 

*********************** 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
  272 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 271
  time to evaluate  : 0.700 
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: 0.9020 (tt) cc_final: 0.8733 (tt)
REVERT: A   64 LYS cc_start: 0.9364 (mtmt) cc_final: 0.9032 (mtmm)
REVERT: A   65 LEU cc_start: 0.9669 (tp) cc_final: 0.9416 (tp)
REVERT: A   76 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8681 (tp40)
REVERT: A   90 MET cc_start: 0.8440 (tmm) cc_final: 0.8128 (tmm)
REVERT: A   92 LEU cc_start: 0.9680 (tt) cc_final: 0.9473 (tt)
REVERT: A   93 GLN cc_start: 0.9232 (tt0) cc_final: 0.8701 (tt0)
REVERT: A   94 GLU cc_start: 0.9022 (pt0) cc_final: 0.8547 (pt0)
REVERT: A   97 GLU cc_start: 0.8756 (mt-10) cc_final: 0.7773 (mt-10)
REVERT: A  106 ASP cc_start: 0.9092 (t70) cc_final: 0.8446 (t70)
REVERT: A  115 LYS cc_start: 0.9246 (mmmt) cc_final: 0.9004 (mmmm)
REVERT: A  130 ILE cc_start: 0.9633 (mm) cc_final: 0.9412 (mm)
REVERT: B   63 GLU cc_start: 0.8687 (tt0) cc_final: 0.8443 (tp30)
REVERT: B   74 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8190 (tm-30)
REVERT: B   85 ASP cc_start: 0.9364 (m-30) cc_final: 0.9102 (m-30)
REVERT: C   90 MET cc_start: 0.9008 (ppp) cc_final: 0.8380 (ppp)
REVERT: C  105 GLU cc_start: 0.8876 (pt0) cc_final: 0.8351 (pp20)
REVERT: C  106 ASP cc_start: 0.8961 (m-30) cc_final: 0.8328 (m-30)
REVERT: D   27 GLN cc_start: 0.9155 (mp10) cc_final: 0.8914 (mp10)
REVERT: D   55 ARG cc_start: 0.9076 (mtt180) cc_final: 0.8373 (mmm-85)
REVERT: D   63 GLU cc_start: 0.9234 (tt0) cc_final: 0.9030 (tm-30)
REVERT: E   60 LEU cc_start: 0.7580 (mt) cc_final: 0.7163 (mt)
REVERT: E   61 LEU cc_start: 0.8820 (mp) cc_final: 0.8214 (tt)
REVERT: E   68 GLN cc_start: 0.9005 (tp-100) cc_final: 0.8405 (tp-100)
REVERT: E   72 ARG cc_start: 0.8997 (ttm-80) cc_final: 0.8705 (mtt-85)
REVERT: E   76 GLN cc_start: 0.9055 (tt0) cc_final: 0.8450 (tp-100)
REVERT: F   29 ILE cc_start: 0.9729 (mm) cc_final: 0.9502 (mm)
REVERT: F   49 LEU cc_start: 0.9359 (tp) cc_final: 0.8636 (tp)
REVERT: F   63 GLU cc_start: 0.9416 (tt0) cc_final: 0.8848 (tm-30)
REVERT: F   64 ASN cc_start: 0.9315 (m-40) cc_final: 0.9111 (m-40)
REVERT: G   61 LEU cc_start: 0.9140 (tt) cc_final: 0.8925 (tt)
REVERT: G   68 GLN cc_start: 0.9295 (pp30) cc_final: 0.9014 (pp30)
REVERT: G   73 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8693 (tm-30)
REVERT: G   93 GLN cc_start: 0.8766 (pt0) cc_final: 0.7828 (pt0)
REVERT: G   94 GLU cc_start: 0.9142 (pt0) cc_final: 0.8692 (pt0)
REVERT: G   97 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8291 (mt-10)
REVERT: G  107 THR cc_start: 0.9745 (p) cc_final: 0.9517 (p)
REVERT: G  123 ASP cc_start: 0.8911 (m-30) cc_final: 0.8400 (t70)
REVERT: G  125 GLN cc_start: 0.9148 (mm-40) cc_final: 0.8906 (tp40)
REVERT: G  128 ARG cc_start: 0.9041 (mtp-110) cc_final: 0.8229 (mtp-110)
REVERT: H   85 ASP cc_start: 0.9203 (m-30) cc_final: 0.8975 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 272
  average time/residue: 0.2839
  time to fit residues: 99.6589
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  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   chunk 73 optimal weight:    9.9990
   chunk 79 optimal weight:   10.0000
   chunk 16 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 33 optimal weight:    6.9990
   chunk 58 optimal weight:   10.0000
   chunk 53 optimal weight:    0.8980
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.060910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.046575 restraints weight = 57743.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.047846 restraints weight = 34516.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.048734 restraints weight = 24328.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          1.1738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10403  Z= 0.243
  Angle     :  0.708   8.859  15068  Z= 0.405
  Chirality :  0.037   0.215   1723
  Planarity :  0.004   0.043   1069
  Dihedral  : 32.848 179.630   3286
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 16.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.33), residues: 578
  helix:  1.07 (0.23), residues: 462
  sheet:  None (None), residues: 0
  loop : -1.30 (0.52), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS B  75 
 PHE   0.022   0.002   PHE G 104 
 TYR   0.011   0.002   TYR D  72 
 ARG   0.014   0.001   ARG H  92 

*********************** 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
  286 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 286
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9406 (mtmt) cc_final: 0.9063 (mtmm)
REVERT: A   65 LEU cc_start: 0.9655 (tp) cc_final: 0.9401 (tp)
REVERT: A   76 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8533 (tp-100)
REVERT: A   90 MET cc_start: 0.8313 (tmm) cc_final: 0.8010 (tmm)
REVERT: A  106 ASP cc_start: 0.8998 (t70) cc_final: 0.8506 (t70)
REVERT: A  115 LYS cc_start: 0.9132 (mmmt) cc_final: 0.8869 (mmmm)
REVERT: A  120 MET cc_start: 0.9171 (mmm) cc_final: 0.8681 (mmm)
REVERT: B   24 ASP cc_start: 0.8756 (t0) cc_final: 0.8341 (t70)
REVERT: B   63 GLU cc_start: 0.8591 (tt0) cc_final: 0.8352 (tp30)
REVERT: B   74 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8185 (tm-30)
REVERT: B   85 ASP cc_start: 0.9210 (m-30) cc_final: 0.8982 (m-30)
REVERT: C   90 MET cc_start: 0.8865 (ppp) cc_final: 0.7996 (ppp)
REVERT: C   97 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8706 (pp20)
REVERT: C  123 ASP cc_start: 0.9061 (m-30) cc_final: 0.8846 (m-30)
REVERT: D   55 ARG cc_start: 0.9021 (mtt180) cc_final: 0.8300 (mmm-85)
REVERT: D   63 GLU cc_start: 0.9272 (tt0) cc_final: 0.9021 (tm-30)
REVERT: D   78 ARG cc_start: 0.7570 (ptm-80) cc_final: 0.7242 (ptm-80)
REVERT: D   82 THR cc_start: 0.8780 (m) cc_final: 0.8451 (m)
REVERT: E   68 GLN cc_start: 0.8901 (tp-100) cc_final: 0.8175 (tp-100)
REVERT: E   72 ARG cc_start: 0.8959 (ttm-80) cc_final: 0.8613 (mtt-85)
REVERT: E   76 GLN cc_start: 0.9043 (tt0) cc_final: 0.8429 (tp-100)
REVERT: E  124 ILE cc_start: 0.9508 (tp) cc_final: 0.9117 (tp)
REVERT: F   29 ILE cc_start: 0.9681 (mm) cc_final: 0.9265 (mm)
REVERT: F   63 GLU cc_start: 0.9376 (tt0) cc_final: 0.8660 (tm-30)
REVERT: F   64 ASN cc_start: 0.9270 (m-40) cc_final: 0.8492 (m-40)
REVERT: F   67 ARG cc_start: 0.9286 (ttp80) cc_final: 0.8357 (ttp-110)
REVERT: F   82 THR cc_start: 0.8300 (p) cc_final: 0.7915 (p)
REVERT: G   73 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8695 (tm-30)
REVERT: G   83 ARG cc_start: 0.8196 (mtp-110) cc_final: 0.7857 (mtp-110)
REVERT: G  107 THR cc_start: 0.9716 (p) cc_final: 0.9431 (p)
REVERT: G  123 ASP cc_start: 0.8871 (m-30) cc_final: 0.8317 (t70)
REVERT: G  125 GLN cc_start: 0.9151 (mm-40) cc_final: 0.8906 (tp40)
REVERT: G  128 ARG cc_start: 0.8977 (mtp-110) cc_final: 0.8191 (mtp-110)
REVERT: H   35 ARG cc_start: 0.8425 (mmt180) cc_final: 0.8007 (mmt180)
REVERT: H   39 ARG cc_start: 0.8752 (mmt90) cc_final: 0.8504 (mmt90)
  outliers start: 0
  outliers final: 0
  residues processed: 286
  average time/residue: 0.2779
  time to fit residues: 103.0771
Evaluate side-chains
  245 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 44 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 28 optimal weight:   20.0000
   chunk 48 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 18 optimal weight:    4.9990
   chunk 14 optimal weight:   10.0000
   chunk 63 optimal weight:   10.0000
   chunk 1 optimal weight:    1.9990
   overall best weight:    3.3588

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 113 HIS
F  27 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.059213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.044889 restraints weight = 59206.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.046126 restraints weight = 35235.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.046951 restraints weight = 24896.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          1.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070  10403  Z= 0.296
  Angle     :  0.719  10.062  15068  Z= 0.415
  Chirality :  0.038   0.203   1723
  Planarity :  0.005   0.059   1069
  Dihedral  : 32.960 179.040   3286
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 18.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.33), residues: 578
  helix:  0.97 (0.23), residues: 460
  sheet:  None (None), residues: 0
  loop : -1.31 (0.51), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS C 113 
 PHE   0.028   0.002   PHE G 104 
 TYR   0.014   0.002   TYR D  72 
 ARG   0.016   0.001   ARG B  35 

*********************** 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
  274 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 274
  time to evaluate  : 0.735 
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: 0.9420 (mtmt) cc_final: 0.9069 (mtmm)
REVERT: A   65 LEU cc_start: 0.9678 (tp) cc_final: 0.9469 (tp)
REVERT: A   73 GLU cc_start: 0.9015 (pp20) cc_final: 0.8728 (pp20)
REVERT: A   90 MET cc_start: 0.8327 (tmm) cc_final: 0.8021 (tmm)
REVERT: A   93 GLN cc_start: 0.9131 (tt0) cc_final: 0.8648 (tt0)
REVERT: A   94 GLU cc_start: 0.8924 (pt0) cc_final: 0.8568 (pt0)
REVERT: A   97 GLU cc_start: 0.8527 (mt-10) cc_final: 0.7396 (mt-10)
REVERT: A  106 ASP cc_start: 0.9233 (t70) cc_final: 0.8941 (t70)
REVERT: A  107 THR cc_start: 0.9728 (p) cc_final: 0.9133 (p)
REVERT: A  115 LYS cc_start: 0.9198 (mmmt) cc_final: 0.8966 (mmmm)
REVERT: A  120 MET cc_start: 0.9177 (mmm) cc_final: 0.8882 (mmm)
REVERT: A  123 ASP cc_start: 0.9009 (m-30) cc_final: 0.8166 (t70)
REVERT: B   24 ASP cc_start: 0.8770 (t0) cc_final: 0.8414 (t0)
REVERT: B   63 GLU cc_start: 0.8669 (tt0) cc_final: 0.8359 (tp30)
REVERT: B   74 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8168 (tm-30)
REVERT: B   85 ASP cc_start: 0.9307 (m-30) cc_final: 0.9048 (m-30)
REVERT: C   63 ARG cc_start: 0.8448 (mmt90) cc_final: 0.8117 (mpt-90)
REVERT: C   77 ASP cc_start: 0.8496 (m-30) cc_final: 0.8144 (m-30)
REVERT: C   78 PHE cc_start: 0.8604 (t80) cc_final: 0.8350 (t80)
REVERT: C   90 MET cc_start: 0.8847 (ppp) cc_final: 0.8328 (ppp)
REVERT: C   93 GLN cc_start: 0.8367 (tm-30) cc_final: 0.8004 (tm-30)
REVERT: C   94 GLU cc_start: 0.9198 (pt0) cc_final: 0.8800 (pp20)
REVERT: C  123 ASP cc_start: 0.9052 (m-30) cc_final: 0.8815 (m-30)
REVERT: D   54 THR cc_start: 0.9327 (p) cc_final: 0.8998 (p)
REVERT: D   55 ARG cc_start: 0.8931 (mtt180) cc_final: 0.8254 (mmm-85)
REVERT: D   63 GLU cc_start: 0.9295 (tt0) cc_final: 0.9015 (tm-30)
REVERT: E   68 GLN cc_start: 0.8904 (tp-100) cc_final: 0.8425 (tp-100)
REVERT: E   72 ARG cc_start: 0.9016 (ttm-80) cc_final: 0.8805 (ttm170)
REVERT: E   76 GLN cc_start: 0.9068 (tt0) cc_final: 0.8520 (tp-100)
REVERT: E  126 LEU cc_start: 0.9287 (tp) cc_final: 0.9020 (tp)
REVERT: F   29 ILE cc_start: 0.9582 (mm) cc_final: 0.9328 (mm)
REVERT: F   63 GLU cc_start: 0.9353 (tt0) cc_final: 0.8753 (tm-30)
REVERT: F   64 ASN cc_start: 0.9330 (m-40) cc_final: 0.8400 (m-40)
REVERT: F   67 ARG cc_start: 0.9297 (ttp80) cc_final: 0.8383 (ttp-110)
REVERT: F   78 ARG cc_start: 0.7531 (ptm160) cc_final: 0.7162 (ptm160)
REVERT: F   82 THR cc_start: 0.8242 (p) cc_final: 0.7904 (p)
REVERT: G   73 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8719 (tm-30)
REVERT: G  107 THR cc_start: 0.9720 (p) cc_final: 0.9504 (p)
REVERT: G  123 ASP cc_start: 0.8943 (m-30) cc_final: 0.8331 (t70)
REVERT: G  125 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8894 (tp40)
REVERT: G  128 ARG cc_start: 0.9022 (mtp-110) cc_final: 0.8171 (mtp-110)
REVERT: H   39 ARG cc_start: 0.8726 (mmt90) cc_final: 0.8458 (mmt90)
REVERT: H   74 GLU cc_start: 0.8926 (tt0) cc_final: 0.8556 (tt0)
REVERT: H   85 ASP cc_start: 0.9265 (m-30) cc_final: 0.8967 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 274
  average time/residue: 0.2661
  time to fit residues: 94.8666
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  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 41 optimal weight:    8.9990
   chunk 12 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 69 optimal weight:   10.0000
   chunk 78 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 16 optimal weight:    5.9990
   chunk 76 optimal weight:   10.0000
   chunk 23 optimal weight:    6.9990
   chunk 44 optimal weight:    7.9990
   chunk 56 optimal weight:   20.0000
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A  93 GLN
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 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 = 0.3293 r_free = 0.3293 target = 0.055852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.042055 restraints weight = 61547.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.043269 restraints weight = 35430.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.044096 restraints weight = 24593.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          1.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.071  10403  Z= 0.395
  Angle     :  0.796  10.797  15068  Z= 0.460
  Chirality :  0.041   0.212   1723
  Planarity :  0.008   0.123   1069
  Dihedral  : 33.336 178.966   3286
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 21.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.33), residues: 578
  helix:  0.78 (0.23), residues: 454
  sheet:  None (None), residues: 0
  loop : -1.54 (0.49), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.003   HIS H  75 
 PHE   0.040   0.004   PHE E  67 
 TYR   0.018   0.002   TYR D  72 
 ARG   0.019   0.001   ARG E  63 

********************** 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
  269 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 269
  time to evaluate  : 0.719 
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: 0.9455 (mtmt) cc_final: 0.9139 (mtmm)
REVERT: A   65 LEU cc_start: 0.9706 (tp) cc_final: 0.9492 (tp)
REVERT: A   90 MET cc_start: 0.8458 (tmm) cc_final: 0.8014 (tmm)
REVERT: A  106 ASP cc_start: 0.9269 (t70) cc_final: 0.8978 (t70)
REVERT: A  115 LYS cc_start: 0.9269 (mmmt) cc_final: 0.9002 (mmmm)
REVERT: A  130 ILE cc_start: 0.9576 (mm) cc_final: 0.9360 (mm)
REVERT: B   24 ASP cc_start: 0.8772 (t0) cc_final: 0.8409 (t0)
REVERT: B   63 GLU cc_start: 0.8780 (tt0) cc_final: 0.8406 (tp30)
REVERT: B   74 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8244 (tm-30)
REVERT: B   85 ASP cc_start: 0.9391 (m-30) cc_final: 0.9065 (m-30)
REVERT: C   63 ARG cc_start: 0.8608 (mmt90) cc_final: 0.8389 (mpt-90)
REVERT: C   78 PHE cc_start: 0.8719 (t80) cc_final: 0.8389 (t80)
REVERT: C   93 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8177 (tm-30)
REVERT: C   94 GLU cc_start: 0.9212 (pt0) cc_final: 0.8947 (pp20)
REVERT: C  123 ASP cc_start: 0.8937 (m-30) cc_final: 0.8723 (m-30)
REVERT: D   35 ARG cc_start: 0.9052 (mtp-110) cc_final: 0.8776 (ttm110)
REVERT: D   55 ARG cc_start: 0.9002 (mtt180) cc_final: 0.8400 (mmm-85)
REVERT: D   63 GLU cc_start: 0.9375 (tt0) cc_final: 0.8994 (tm-30)
REVERT: D   64 ASN cc_start: 0.9202 (m-40) cc_final: 0.8957 (p0)
REVERT: D   77 LYS cc_start: 0.7725 (mppt) cc_final: 0.7396 (mmtt)
REVERT: D   93 GLN cc_start: 0.9107 (tm-30) cc_final: 0.8827 (tm-30)
REVERT: E   76 GLN cc_start: 0.9127 (tt0) cc_final: 0.8636 (tp-100)
REVERT: E  126 LEU cc_start: 0.9398 (tp) cc_final: 0.9087 (tp)
REVERT: F   63 GLU cc_start: 0.9424 (tt0) cc_final: 0.9009 (tm-30)
REVERT: F   64 ASN cc_start: 0.9406 (m-40) cc_final: 0.8792 (m-40)
REVERT: G   68 GLN cc_start: 0.9266 (pp30) cc_final: 0.9043 (pp30)
REVERT: G   73 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8769 (tm-30)
REVERT: G   94 GLU cc_start: 0.8990 (pt0) cc_final: 0.8759 (pt0)
REVERT: G  120 MET cc_start: 0.8664 (mmp) cc_final: 0.8390 (mmm)
REVERT: G  123 ASP cc_start: 0.8933 (m-30) cc_final: 0.8448 (t70)
REVERT: G  125 GLN cc_start: 0.9230 (mm-40) cc_final: 0.8833 (tp40)
REVERT: G  128 ARG cc_start: 0.8917 (mtp-110) cc_final: 0.8159 (mtp-110)
REVERT: H   27 GLN cc_start: 0.8965 (mp10) cc_final: 0.8711 (mp10)
REVERT: H   35 ARG cc_start: 0.8430 (mmt180) cc_final: 0.8047 (mmt180)
REVERT: H   39 ARG cc_start: 0.8716 (mmt90) cc_final: 0.8468 (mmt90)
REVERT: H   74 GLU cc_start: 0.9057 (tt0) cc_final: 0.8669 (tt0)
REVERT: H   85 ASP cc_start: 0.9396 (m-30) cc_final: 0.9041 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 269
  average time/residue: 0.2690
  time to fit residues: 93.6201
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  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 47 optimal weight:    0.0980
   chunk 27 optimal weight:    7.9990
   chunk 79 optimal weight:   10.0000
   chunk 63 optimal weight:   10.0000
   chunk 34 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   chunk 76 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 62 optimal weight:   10.0000
   chunk 19 optimal weight:   10.0000
   overall best weight:    7.4188

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A  93 GLN
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  75 HIS
F  27 GLN
** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.053159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.040009 restraints weight = 60211.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.041160 restraints weight = 35392.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.041929 restraints weight = 24699.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          1.3637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.082  10403  Z= 0.480
  Angle     :  0.855  12.230  15068  Z= 0.498
  Chirality :  0.044   0.223   1723
  Planarity :  0.008   0.126   1069
  Dihedral  : 33.917 179.065   3286
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 25.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.40 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.32), residues: 578
  helix:  0.40 (0.23), residues: 453
  sheet:  None (None), residues: 0
  loop : -1.57 (0.49), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.004   HIS H  75 
 PHE   0.034   0.004   PHE G 104 
 TYR   0.019   0.003   TYR H  88 
 ARG   0.021   0.001   ARG E  63 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2880.11 seconds
wall clock time: 52 minutes 19.03 seconds (3139.03 seconds total)