Starting phenix.real_space_refine
on Sat Dec 28 23:55:32 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yoz_33991/12_2024/7yoz_33991.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yoz_33991/12_2024/7yoz_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_33991/12_2024/7yoz_33991.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yoz_33991/12_2024/7yoz_33991.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yoz_33991/12_2024/7yoz_33991.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yoz_33991/12_2024/7yoz_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-5532/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: 5.85, per 1000 atoms: 0.60
  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: 2.57
  Conformation dependent library (CDL) restraints added in 660.0 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: 4.65
  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: 3.70

  Time building geometry restraints manager: 2.97 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:             0.260
  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:          0.390
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     27.960
  Find NCS groups from input model:        0.280
  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:             0.010
  Load rotamer database and sin/cos tables:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.090
-------------------------------------------------------------------------------
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  : 0.687 
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: 0.3505
  time to fit residues: 143.7083
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  : 0.657 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
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  : 0.754 
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: 0.7787 (tt) cc_final: 0.7475 (tt)
REVERT: A   64 LYS cc_start: 0.9219 (mttm) cc_final: 0.8762 (mtmm)
REVERT: A   85 GLN cc_start: 0.8952 (tt0) cc_final: 0.8486 (tp40)
REVERT: A   93 GLN cc_start: 0.8868 (tt0) cc_final: 0.8003 (tm-30)
REVERT: A   96 CYS cc_start: 0.9004 (m) cc_final: 0.8651 (m)
REVERT: A  119 ILE cc_start: 0.9071 (pt) cc_final: 0.8777 (mt)
REVERT: A  123 ASP cc_start: 0.8832 (m-30) cc_final: 0.8330 (t70)
REVERT: A  130 ILE cc_start: 0.9746 (mt) cc_final: 0.9491 (mm)
REVERT: B   24 ASP cc_start: 0.8156 (t0) cc_final: 0.7519 (p0)
REVERT: C   90 MET cc_start: 0.9214 (ppp) cc_final: 0.8766 (ppp)
REVERT: C   93 GLN cc_start: 0.9077 (tm-30) cc_final: 0.8841 (tm-30)
REVERT: C   94 GLU cc_start: 0.9206 (pt0) cc_final: 0.8872 (pt0)
REVERT: C  100 LEU cc_start: 0.9443 (tp) cc_final: 0.9090 (tp)
REVERT: C  104 PHE cc_start: 0.9001 (m-80) cc_final: 0.8441 (m-80)
REVERT: C  106 ASP cc_start: 0.9113 (m-30) cc_final: 0.8556 (m-30)
REVERT: C  129 ARG cc_start: 0.8240 (tpm170) cc_final: 0.7703 (tpm170)
REVERT: D   49 LEU cc_start: 0.8321 (pp) cc_final: 0.7972 (pt)
REVERT: D   55 ARG cc_start: 0.8919 (mtt180) cc_final: 0.8480 (mmm-85)
REVERT: D   59 LYS cc_start: 0.9134 (tttt) cc_final: 0.8349 (tptp)
REVERT: D   66 ILE cc_start: 0.9074 (mm) cc_final: 0.8833 (pt)
REVERT: E   87 SER cc_start: 0.8957 (m) cc_final: 0.8508 (p)
REVERT: E   93 GLN cc_start: 0.9245 (mm110) cc_final: 0.8929 (tp40)
REVERT: E  120 MET cc_start: 0.8609 (mmp) cc_final: 0.8085 (mmm)
REVERT: E  123 ASP cc_start: 0.9014 (m-30) cc_final: 0.8769 (m-30)
REVERT: E  128 ARG cc_start: 0.8957 (mmm-85) cc_final: 0.8256 (mmm-85)
REVERT: E  129 ARG cc_start: 0.8595 (tmt-80) cc_final: 0.8215 (tpm170)
REVERT: F   63 GLU cc_start: 0.8799 (tt0) cc_final: 0.8347 (tm-30)
REVERT: G   68 GLN cc_start: 0.8950 (tm130) cc_final: 0.8480 (tm-30)
REVERT: G   90 MET cc_start: 0.8552 (ttm) cc_final: 0.8216 (tmm)
REVERT: G   96 CYS cc_start: 0.8087 (m) cc_final: 0.7744 (m)
REVERT: G   97 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7793 (mt-10)
REVERT: G  123 ASP cc_start: 0.8760 (m-30) cc_final: 0.8326 (t70)
REVERT: G  128 ARG cc_start: 0.9158 (mtp-110) cc_final: 0.8956 (mtp-110)
REVERT: H   46 ILE cc_start: 0.8748 (mp) cc_final: 0.8520 (mt)
REVERT: H   74 GLU cc_start: 0.9053 (tt0) cc_final: 0.8590 (tt0)
  outliers start: 3
  outliers final: 0
  residues processed: 262
  average time/residue: 0.3228
  time to fit residues: 105.5388
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  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 40 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   chunk 60 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9980
   chunk 20 optimal weight:    7.9990
   chunk 72 optimal weight:   10.0000
   chunk 78 optimal weight:   10.0000
   chunk 64 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 58 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   overall best weight:    5.3988

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

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.8666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.093  10403  Z= 0.404
  Angle     :  0.786   6.799  15068  Z= 0.458
  Chirality :  0.042   0.290   1723
  Planarity :  0.007   0.067   1069
  Dihedral  : 32.780 178.968   3286
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 20.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  6.15 %
    Favored  : 93.25 %
  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:  0.91 (0.32), residues: 578
  helix:  1.15 (0.23), residues: 454
  sheet:  None (None), residues: 0
  loop : -1.29 (0.45), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.003   HIS A 113 
 PHE   0.018   0.003   PHE G 104 
 TYR   0.018   0.002   TYR B  88 
 ARG   0.018   0.001   ARG A  63 

*********************** 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
  288 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 285
  time to evaluate  : 0.789 
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   60 LEU cc_start: 0.8983 (mm) cc_final: 0.8705 (mt)
REVERT: A   64 LYS cc_start: 0.9452 (mttm) cc_final: 0.9194 (mtmm)
REVERT: A   68 GLN cc_start: 0.9354 (tp-100) cc_final: 0.8682 (tm-30)
REVERT: A   90 MET cc_start: 0.8230 (tmm) cc_final: 0.7773 (tmm)
REVERT: A   93 GLN cc_start: 0.9136 (tt0) cc_final: 0.7869 (tm-30)
REVERT: A   94 GLU cc_start: 0.9097 (pt0) cc_final: 0.8374 (pt0)
REVERT: A   97 GLU cc_start: 0.8309 (mt-10) cc_final: 0.6984 (mt-10)
REVERT: A  115 LYS cc_start: 0.9008 (mmmt) cc_final: 0.8632 (mmmm)
REVERT: A  119 ILE cc_start: 0.9441 (pt) cc_final: 0.9143 (mt)
REVERT: A  120 MET cc_start: 0.9037 (mmm) cc_final: 0.8710 (mmm)
REVERT: A  130 ILE cc_start: 0.9736 (mt) cc_final: 0.9419 (mt)
REVERT: B   24 ASP cc_start: 0.8624 (t0) cc_final: 0.8372 (t0)
REVERT: B   52 GLU cc_start: 0.8908 (tp30) cc_final: 0.8669 (tp30)
REVERT: B   63 GLU cc_start: 0.8707 (tt0) cc_final: 0.8186 (tp30)
REVERT: B   74 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8222 (tm-30)
REVERT: B   85 ASP cc_start: 0.9337 (m-30) cc_final: 0.9117 (m-30)
REVERT: B   92 ARG cc_start: 0.8019 (ttt180) cc_final: 0.7779 (tmm-80)
REVERT: C   78 PHE cc_start: 0.8476 (t80) cc_final: 0.8045 (t80)
REVERT: C   90 MET cc_start: 0.9107 (ppp) cc_final: 0.8521 (ppp)
REVERT: C   93 GLN cc_start: 0.9191 (tm-30) cc_final: 0.8789 (tm-30)
REVERT: C  106 ASP cc_start: 0.9215 (m-30) cc_final: 0.8502 (m-30)
REVERT: C  129 ARG cc_start: 0.8646 (tpm170) cc_final: 0.8186 (tpm170)
REVERT: D   52 GLU cc_start: 0.9000 (pp20) cc_final: 0.8688 (pp20)
REVERT: D   55 ARG cc_start: 0.9179 (mtt180) cc_final: 0.8555 (mmm-85)
REVERT: D   59 LYS cc_start: 0.9473 (tttt) cc_final: 0.8609 (tptp)
REVERT: E   76 GLN cc_start: 0.8872 (tt0) cc_final: 0.8291 (tp-100)
REVERT: E   90 MET cc_start: 0.8585 (ppp) cc_final: 0.8111 (ppp)
REVERT: E   93 GLN cc_start: 0.9322 (mm110) cc_final: 0.9030 (mm110)
REVERT: E  119 ILE cc_start: 0.8719 (pt) cc_final: 0.8271 (pt)
REVERT: E  120 MET cc_start: 0.8646 (mmp) cc_final: 0.8230 (mmm)
REVERT: E  123 ASP cc_start: 0.9022 (m-30) cc_final: 0.8766 (m-30)
REVERT: F   49 LEU cc_start: 0.9355 (tt) cc_final: 0.8185 (tp)
REVERT: F   50 ILE cc_start: 0.9610 (tp) cc_final: 0.9160 (mm)
REVERT: F   54 THR cc_start: 0.9493 (m) cc_final: 0.9155 (p)
REVERT: F   55 ARG cc_start: 0.8800 (mmm-85) cc_final: 0.8179 (mmm-85)
REVERT: F   63 GLU cc_start: 0.9236 (tt0) cc_final: 0.9004 (tm-30)
REVERT: F   64 ASN cc_start: 0.9123 (t0) cc_final: 0.8891 (t0)
REVERT: F   84 MET cc_start: 0.8735 (ptt) cc_final: 0.8471 (ptt)
REVERT: F   88 TYR cc_start: 0.9067 (m-80) cc_final: 0.8542 (t80)
REVERT: G   60 LEU cc_start: 0.8695 (mm) cc_final: 0.8100 (mm)
REVERT: G   61 LEU cc_start: 0.9184 (tt) cc_final: 0.8522 (tt)
REVERT: G   65 LEU cc_start: 0.9398 (tp) cc_final: 0.9190 (tp)
REVERT: G   73 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8729 (tm-30)
REVERT: G   90 MET cc_start: 0.8912 (ttm) cc_final: 0.8368 (tmm)
REVERT: G   93 GLN cc_start: 0.8993 (pt0) cc_final: 0.7792 (pt0)
REVERT: G   94 GLU cc_start: 0.8894 (pt0) cc_final: 0.8606 (pt0)
REVERT: G   97 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7947 (mt-10)
REVERT: G  123 ASP cc_start: 0.8883 (m-30) cc_final: 0.8597 (t70)
REVERT: G  128 ARG cc_start: 0.9219 (mtp-110) cc_final: 0.8918 (mtp-110)
REVERT: H   35 ARG cc_start: 0.8303 (mmt180) cc_final: 0.7984 (mmt180)
REVERT: H   39 ARG cc_start: 0.8846 (mmt90) cc_final: 0.8597 (mmt-90)
REVERT: H   88 TYR cc_start: 0.8744 (m-10) cc_final: 0.8364 (m-10)
  outliers start: 3
  outliers final: 0
  residues processed: 286
  average time/residue: 0.3228
  time to fit residues: 115.5156
Evaluate side-chains
  237 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 73 optimal weight:    7.9990
   chunk 77 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9990
   chunk 69 optimal weight:   10.0000
   chunk 20 optimal weight:    0.0040
   chunk 64 optimal weight:   10.0000
   overall best weight:    1.1798

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
E  93 GLN
E 113 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.8814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10403  Z= 0.210
  Angle     :  0.635   6.452  15068  Z= 0.374
  Chirality :  0.035   0.154   1723
  Planarity :  0.004   0.041   1069
  Dihedral  : 32.205 178.661   3286
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  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:  1.43 (0.23), residues: 459
  sheet:  None (None), residues: 0
  loop : -1.00 (0.46), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 113 
 PHE   0.019   0.002   PHE G 104 
 TYR   0.010   0.001   TYR F  51 
 ARG   0.008   0.001   ARG H  92 

*********************** 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
  290 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 290
  time to evaluate  : 0.703 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 LEU cc_start: 0.9502 (tp) cc_final: 0.9279 (tp)
REVERT: A   68 GLN cc_start: 0.8978 (tp40) cc_final: 0.8660 (tp40)
REVERT: A   90 MET cc_start: 0.8176 (tmm) cc_final: 0.7780 (tmm)
REVERT: A  120 MET cc_start: 0.9120 (mmm) cc_final: 0.8807 (mmm)
REVERT: B   24 ASP cc_start: 0.8422 (t0) cc_final: 0.7893 (p0)
REVERT: B   29 ILE cc_start: 0.9384 (pt) cc_final: 0.9118 (mt)
REVERT: B   39 ARG cc_start: 0.8738 (mmm-85) cc_final: 0.8505 (mpp80)
REVERT: B   63 GLU cc_start: 0.8653 (tt0) cc_final: 0.8051 (tp30)
REVERT: B   74 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7855 (tm-30)
REVERT: C   64 LYS cc_start: 0.8955 (mmmm) cc_final: 0.8603 (mmmm)
REVERT: C   78 PHE cc_start: 0.8438 (t80) cc_final: 0.8134 (t80)
REVERT: C   90 MET cc_start: 0.8989 (ppp) cc_final: 0.8242 (ppp)
REVERT: C   94 GLU cc_start: 0.9211 (pt0) cc_final: 0.8706 (pt0)
REVERT: C  106 ASP cc_start: 0.8907 (m-30) cc_final: 0.8546 (m-30)
REVERT: C  123 ASP cc_start: 0.9221 (m-30) cc_final: 0.8992 (m-30)
REVERT: C  130 ILE cc_start: 0.8964 (mm) cc_final: 0.8731 (mm)
REVERT: D   49 LEU cc_start: 0.8603 (pt) cc_final: 0.8052 (pt)
REVERT: D   55 ARG cc_start: 0.9171 (mtt180) cc_final: 0.8526 (mmm-85)
REVERT: D   63 GLU cc_start: 0.9382 (pt0) cc_final: 0.9022 (pp20)
REVERT: D   66 ILE cc_start: 0.9431 (mt) cc_final: 0.9201 (pt)
REVERT: D   72 TYR cc_start: 0.8140 (t80) cc_final: 0.7846 (t80)
REVERT: D   84 MET cc_start: 0.9044 (mmm) cc_final: 0.8530 (ppp)
REVERT: E   68 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8391 (tp-100)
REVERT: E   76 GLN cc_start: 0.9018 (tt0) cc_final: 0.8476 (tp-100)
REVERT: E   86 SER cc_start: 0.8526 (t) cc_final: 0.7565 (t)
REVERT: E  110 CYS cc_start: 0.8947 (t) cc_final: 0.8419 (t)
REVERT: E  119 ILE cc_start: 0.8795 (pt) cc_final: 0.8495 (pt)
REVERT: F   50 ILE cc_start: 0.9349 (tp) cc_final: 0.9041 (mm)
REVERT: F   54 THR cc_start: 0.9520 (m) cc_final: 0.9314 (p)
REVERT: F   90 LEU cc_start: 0.8874 (tt) cc_final: 0.8548 (pp)
REVERT: G   60 LEU cc_start: 0.8454 (mm) cc_final: 0.8004 (mt)
REVERT: G   61 LEU cc_start: 0.9091 (tt) cc_final: 0.8518 (tt)
REVERT: G   90 MET cc_start: 0.8828 (ttm) cc_final: 0.8310 (tmm)
REVERT: G   93 GLN cc_start: 0.8507 (pt0) cc_final: 0.7791 (pt0)
REVERT: G   94 GLU cc_start: 0.8696 (pt0) cc_final: 0.8262 (pt0)
REVERT: G   97 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7848 (mt-10)
REVERT: G  107 THR cc_start: 0.9648 (p) cc_final: 0.9214 (p)
REVERT: G  123 ASP cc_start: 0.8834 (m-30) cc_final: 0.8305 (t70)
REVERT: G  128 ARG cc_start: 0.9025 (mtp-110) cc_final: 0.8538 (mtp-110)
REVERT: H   35 ARG cc_start: 0.8266 (mmt180) cc_final: 0.7977 (mmt180)
REVERT: H   50 ILE cc_start: 0.9266 (mm) cc_final: 0.8877 (mm)
REVERT: H   74 GLU cc_start: 0.8960 (tt0) cc_final: 0.8532 (tt0)
REVERT: H   88 TYR cc_start: 0.8462 (m-10) cc_final: 0.8014 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 290
  average time/residue: 0.2937
  time to fit residues: 107.7539
Evaluate side-chains
  243 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 65 optimal weight:   10.0000
   chunk 53 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    7.9990
   chunk 69 optimal weight:   10.0000
   chunk 19 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    4.5990

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          1.0181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064  10403  Z= 0.353
  Angle     :  0.707   5.318  15068  Z= 0.419
  Chirality :  0.038   0.146   1723
  Planarity :  0.006   0.078   1069
  Dihedral  : 32.739 179.219   3286
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 20.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.05 (0.33), residues: 578
  helix:  1.19 (0.23), residues: 459
  sheet:  None (None), residues: 0
  loop : -1.08 (0.48), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS A 113 
 PHE   0.016   0.002   PHE C  67 
 TYR   0.011   0.002   TYR D  72 
 ARG   0.008   0.001   ARG C 116 

*********************** 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
  262 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9256 (mtmt) cc_final: 0.8926 (mtmm)
REVERT: A   65 LEU cc_start: 0.9609 (tp) cc_final: 0.9388 (tp)
REVERT: A   68 GLN cc_start: 0.9242 (tp40) cc_final: 0.8825 (tp-100)
REVERT: A   90 MET cc_start: 0.8272 (tmm) cc_final: 0.7975 (tmm)
REVERT: A   97 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8193 (mt-10)
REVERT: A  106 ASP cc_start: 0.9351 (t70) cc_final: 0.8908 (t70)
REVERT: A  115 LYS cc_start: 0.9144 (mmmt) cc_final: 0.8740 (mmmm)
REVERT: A  120 MET cc_start: 0.9191 (mmm) cc_final: 0.8946 (mmm)
REVERT: B   24 ASP cc_start: 0.8551 (t0) cc_final: 0.8258 (t0)
REVERT: B   63 GLU cc_start: 0.8728 (tt0) cc_final: 0.8246 (tp30)
REVERT: B   74 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8061 (tm-30)
REVERT: B   85 ASP cc_start: 0.9206 (m-30) cc_final: 0.8991 (m-30)
REVERT: C   78 PHE cc_start: 0.8528 (t80) cc_final: 0.8181 (t80)
REVERT: C   90 MET cc_start: 0.8979 (ppp) cc_final: 0.8403 (ppp)
REVERT: C   97 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8704 (pp20)
REVERT: C  120 MET cc_start: 0.6934 (mpp) cc_final: 0.6695 (mpp)
REVERT: C  123 ASP cc_start: 0.9219 (m-30) cc_final: 0.8947 (m-30)
REVERT: D   35 ARG cc_start: 0.9022 (mmm-85) cc_final: 0.8778 (ttm110)
REVERT: D   55 ARG cc_start: 0.9121 (mtt180) cc_final: 0.8402 (mmm-85)
REVERT: D   60 VAL cc_start: 0.9234 (p) cc_final: 0.8568 (p)
REVERT: D   63 GLU cc_start: 0.9359 (pt0) cc_final: 0.9086 (pp20)
REVERT: E   60 LEU cc_start: 0.6829 (mt) cc_final: 0.6345 (mt)
REVERT: E   61 LEU cc_start: 0.8961 (mp) cc_final: 0.7999 (tt)
REVERT: E   76 GLN cc_start: 0.8998 (tt0) cc_final: 0.8442 (tp-100)
REVERT: E   90 MET cc_start: 0.8830 (ptp) cc_final: 0.8309 (ppp)
REVERT: E   94 GLU cc_start: 0.9060 (pt0) cc_final: 0.8276 (pt0)
REVERT: E  110 CYS cc_start: 0.8925 (t) cc_final: 0.8589 (t)
REVERT: F   29 ILE cc_start: 0.9563 (mm) cc_final: 0.9354 (mm)
REVERT: F   35 ARG cc_start: 0.8910 (mmm-85) cc_final: 0.8704 (ttm-80)
REVERT: F   50 ILE cc_start: 0.9432 (tp) cc_final: 0.9023 (mm)
REVERT: F   60 VAL cc_start: 0.8949 (p) cc_final: 0.8534 (p)
REVERT: F   78 ARG cc_start: 0.7093 (ptm160) cc_final: 0.6859 (ptm160)
REVERT: G  106 ASP cc_start: 0.9138 (t70) cc_final: 0.8728 (t70)
REVERT: G  107 THR cc_start: 0.9737 (p) cc_final: 0.9442 (p)
REVERT: G  120 MET cc_start: 0.9126 (mmm) cc_final: 0.8862 (mmm)
REVERT: G  123 ASP cc_start: 0.8847 (m-30) cc_final: 0.8486 (t70)
REVERT: G  128 ARG cc_start: 0.8984 (mtp-110) cc_final: 0.8187 (mtp-110)
REVERT: H   39 ARG cc_start: 0.8755 (mmt90) cc_final: 0.8362 (mmt90)
REVERT: H   63 GLU cc_start: 0.8533 (tt0) cc_final: 0.8058 (tp30)
REVERT: H   88 TYR cc_start: 0.8733 (m-10) cc_final: 0.8052 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 262
  average time/residue: 0.2952
  time to fit residues: 98.6518
Evaluate side-chains
  226 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 19 optimal weight:    9.9990
   chunk 77 optimal weight:   10.0000
   chunk 64 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
F  27 GLN
G  68 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: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          1.0454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10403  Z= 0.241
  Angle     :  0.671  14.367  15068  Z= 0.390
  Chirality :  0.036   0.164   1723
  Planarity :  0.004   0.035   1069
  Dihedral  : 32.517 179.329   3286
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 17.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.24), residues: 456
  sheet:  None (None), residues: 0
  loop : -1.11 (0.47), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS A 113 
 PHE   0.023   0.002   PHE G 104 
 TYR   0.008   0.001   TYR D  51 
 ARG   0.010   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
  266 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 0.666 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9344 (mtmt) cc_final: 0.8840 (mtmm)
REVERT: A   65 LEU cc_start: 0.9626 (tp) cc_final: 0.9388 (tp)
REVERT: A   90 MET cc_start: 0.8320 (tmm) cc_final: 0.7924 (tmm)
REVERT: A   93 GLN cc_start: 0.9004 (mt0) cc_final: 0.8428 (mt0)
REVERT: A   94 GLU cc_start: 0.8997 (pt0) cc_final: 0.8627 (pt0)
REVERT: A   97 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7713 (mp0)
REVERT: A  106 ASP cc_start: 0.9318 (t70) cc_final: 0.8881 (t70)
REVERT: A  115 LYS cc_start: 0.9098 (mmmt) cc_final: 0.8729 (mmmm)
REVERT: B   24 ASP cc_start: 0.8797 (t0) cc_final: 0.8153 (t0)
REVERT: B   44 LYS cc_start: 0.9231 (mppt) cc_final: 0.8927 (mmmm)
REVERT: B   63 GLU cc_start: 0.8682 (tt0) cc_final: 0.8234 (tp30)
REVERT: B   74 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7720 (tm-30)
REVERT: C   64 LYS cc_start: 0.8937 (mmmm) cc_final: 0.8535 (mmmm)
REVERT: C   78 PHE cc_start: 0.8540 (t80) cc_final: 0.8170 (t80)
REVERT: C   90 MET cc_start: 0.8936 (ppp) cc_final: 0.8400 (ppp)
REVERT: C  105 GLU cc_start: 0.8850 (pt0) cc_final: 0.8620 (pp20)
REVERT: C  106 ASP cc_start: 0.8400 (m-30) cc_final: 0.7804 (m-30)
REVERT: C  120 MET cc_start: 0.7084 (mpp) cc_final: 0.6820 (mpp)
REVERT: C  123 ASP cc_start: 0.9155 (m-30) cc_final: 0.8793 (m-30)
REVERT: D   55 ARG cc_start: 0.9105 (mtt180) cc_final: 0.8265 (mmm-85)
REVERT: D   60 VAL cc_start: 0.9233 (p) cc_final: 0.8581 (p)
REVERT: D   63 GLU cc_start: 0.9368 (pt0) cc_final: 0.9030 (pp20)
REVERT: D   78 ARG cc_start: 0.7767 (ptm-80) cc_final: 0.7519 (ptm-80)
REVERT: E   61 LEU cc_start: 0.8865 (mp) cc_final: 0.8587 (mt)
REVERT: E   76 GLN cc_start: 0.8977 (tt0) cc_final: 0.8433 (tp-100)
REVERT: E   86 SER cc_start: 0.8299 (t) cc_final: 0.7549 (t)
REVERT: E   90 MET cc_start: 0.8835 (ptp) cc_final: 0.8481 (ptp)
REVERT: E  110 CYS cc_start: 0.8859 (t) cc_final: 0.8549 (t)
REVERT: E  134 ARG cc_start: 0.7569 (mmp80) cc_final: 0.7312 (mmp80)
REVERT: F   29 ILE cc_start: 0.9501 (mm) cc_final: 0.9055 (mm)
REVERT: F   60 VAL cc_start: 0.9005 (p) cc_final: 0.8499 (p)
REVERT: F   78 ARG cc_start: 0.7204 (ptm160) cc_final: 0.6891 (ptm160)
REVERT: F   82 THR cc_start: 0.7983 (p) cc_final: 0.7727 (p)
REVERT: G   61 LEU cc_start: 0.9112 (tt) cc_final: 0.8763 (tt)
REVERT: G   94 GLU cc_start: 0.8668 (pt0) cc_final: 0.8362 (pt0)
REVERT: G   97 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7992 (mt-10)
REVERT: G  106 ASP cc_start: 0.9084 (t70) cc_final: 0.8516 (t70)
REVERT: G  128 ARG cc_start: 0.8974 (mtp-110) cc_final: 0.8270 (mtp-110)
REVERT: H   39 ARG cc_start: 0.8767 (mmt90) cc_final: 0.8353 (mmt90)
REVERT: H   88 TYR cc_start: 0.8494 (m-10) cc_final: 0.7816 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 266
  average time/residue: 0.2923
  time to fit residues: 98.9493
Evaluate side-chains
  233 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 44 optimal weight:    8.9990
   chunk 56 optimal weight:   20.0000
   chunk 43 optimal weight:    1.9990
   chunk 65 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   chunk 48 optimal weight:    7.9990
   chunk 47 optimal weight:    4.9990
   chunk 35 optimal weight:   10.0000
   chunk 30 optimal weight:    0.1980
   chunk 46 optimal weight:    0.8980
   overall best weight:    2.4186

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          1.0762

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= 0.252
  Angle     :  0.664   9.838  15068  Z= 0.391
  Chirality :  0.036   0.164   1723
  Planarity :  0.004   0.040   1069
  Dihedral  : 32.481 179.587   3286
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 17.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.98 %
    Favored  : 97.82 %
  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:  1.20 (0.33), residues: 578
  helix:  1.37 (0.24), residues: 452
  sheet:  None (None), residues: 0
  loop : -1.21 (0.48), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS B  75 
 PHE   0.024   0.002   PHE G 104 
 TYR   0.016   0.002   TYR D  72 
 ARG   0.013   0.001   ARG H  92 

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

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 266
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9333 (mtmt) cc_final: 0.8834 (mtmm)
REVERT: A   65 LEU cc_start: 0.9609 (tp) cc_final: 0.9366 (tp)
REVERT: A   68 GLN cc_start: 0.9008 (tp-100) cc_final: 0.7596 (tp40)
REVERT: A   90 MET cc_start: 0.8225 (tmm) cc_final: 0.7924 (tmm)
REVERT: A   93 GLN cc_start: 0.8976 (mt0) cc_final: 0.8427 (mt0)
REVERT: A   97 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7707 (mp0)
REVERT: A  106 ASP cc_start: 0.9268 (t70) cc_final: 0.8854 (t70)
REVERT: A  115 LYS cc_start: 0.9106 (mmmt) cc_final: 0.8791 (mmmm)
REVERT: B   24 ASP cc_start: 0.8474 (t0) cc_final: 0.8254 (t0)
REVERT: B   63 GLU cc_start: 0.8693 (tt0) cc_final: 0.8339 (tp30)
REVERT: C   64 LYS cc_start: 0.8931 (mmmm) cc_final: 0.8604 (mmmm)
REVERT: C   78 PHE cc_start: 0.8576 (t80) cc_final: 0.8040 (t80)
REVERT: C   90 MET cc_start: 0.8998 (ppp) cc_final: 0.8351 (ppp)
REVERT: C  105 GLU cc_start: 0.8833 (pt0) cc_final: 0.8553 (pp20)
REVERT: C  106 ASP cc_start: 0.8528 (m-30) cc_final: 0.7819 (m-30)
REVERT: C  120 MET cc_start: 0.7074 (mpp) cc_final: 0.6871 (mpp)
REVERT: C  123 ASP cc_start: 0.9193 (m-30) cc_final: 0.8842 (m-30)
REVERT: D   55 ARG cc_start: 0.9102 (mtt180) cc_final: 0.8245 (mmm-85)
REVERT: D   60 VAL cc_start: 0.9246 (p) cc_final: 0.8642 (p)
REVERT: D   78 ARG cc_start: 0.7789 (ptm-80) cc_final: 0.7532 (ptm-80)
REVERT: E   64 LYS cc_start: 0.8620 (mmmt) cc_final: 0.7964 (mmmm)
REVERT: E   68 GLN cc_start: 0.9194 (tp40) cc_final: 0.8777 (tp40)
REVERT: E   76 GLN cc_start: 0.8984 (tt0) cc_final: 0.8464 (tp-100)
REVERT: E  110 CYS cc_start: 0.8888 (t) cc_final: 0.8512 (t)
REVERT: F   60 VAL cc_start: 0.8976 (p) cc_final: 0.8470 (p)
REVERT: F   67 ARG cc_start: 0.8987 (ttp-110) cc_final: 0.8185 (ttp-110)
REVERT: F   78 ARG cc_start: 0.7183 (ptm160) cc_final: 0.6858 (ptm160)
REVERT: F   82 THR cc_start: 0.7963 (p) cc_final: 0.7623 (p)
REVERT: G  106 ASP cc_start: 0.9090 (t70) cc_final: 0.8572 (t70)
REVERT: G  128 ARG cc_start: 0.8884 (mtp-110) cc_final: 0.8168 (mtp-110)
REVERT: H   35 ARG cc_start: 0.8372 (mmt180) cc_final: 0.7908 (tpt170)
REVERT: H   39 ARG cc_start: 0.8763 (mmt90) cc_final: 0.8105 (mmt90)
REVERT: H   46 ILE cc_start: 0.9468 (mp) cc_final: 0.9243 (mt)
REVERT: H   78 ARG cc_start: 0.8653 (ptt-90) cc_final: 0.8250 (ptt-90)
REVERT: H   85 ASP cc_start: 0.9025 (m-30) cc_final: 0.8788 (m-30)
REVERT: H   88 TYR cc_start: 0.8443 (m-10) cc_final: 0.8031 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 267
  average time/residue: 0.3023
  time to fit residues: 103.4778
Evaluate side-chains
  235 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 15 optimal weight:    8.9990
   chunk 14 optimal weight:   10.0000
   chunk 49 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 60 optimal weight:   10.0000
   chunk 70 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 67 optimal weight:   10.0000
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  68 GLN
** G  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          1.1297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  10403  Z= 0.281
  Angle     :  0.691   8.642  15068  Z= 0.403
  Chirality :  0.037   0.152   1723
  Planarity :  0.005   0.039   1069
  Dihedral  : 32.629 179.452   3286
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 18.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.90 (0.34), residues: 578
  helix:  1.19 (0.24), residues: 459
  sheet:  None (None), residues: 0
  loop : -1.63 (0.45), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS A 113 
 PHE   0.026   0.002   PHE G 104 
 TYR   0.012   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
  270 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 270
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9332 (mtmt) cc_final: 0.8863 (mtmm)
REVERT: A   65 LEU cc_start: 0.9606 (tp) cc_final: 0.9314 (tp)
REVERT: A   72 ARG cc_start: 0.8832 (mpt90) cc_final: 0.8419 (mpt90)
REVERT: A   90 MET cc_start: 0.8214 (tmm) cc_final: 0.7729 (tmm)
REVERT: A   93 GLN cc_start: 0.9000 (mt0) cc_final: 0.8436 (mt0)
REVERT: A   94 GLU cc_start: 0.9023 (pt0) cc_final: 0.8605 (pt0)
REVERT: A   97 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7684 (mp0)
REVERT: A  106 ASP cc_start: 0.9313 (t70) cc_final: 0.8898 (t70)
REVERT: A  115 LYS cc_start: 0.9177 (mmmt) cc_final: 0.8904 (mmmm)
REVERT: B   24 ASP cc_start: 0.8515 (t0) cc_final: 0.8149 (t0)
REVERT: B   63 GLU cc_start: 0.8677 (tt0) cc_final: 0.8453 (tp30)
REVERT: B   74 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7979 (tm-30)
REVERT: C   64 LYS cc_start: 0.8938 (mmmm) cc_final: 0.8572 (mmmm)
REVERT: C   78 PHE cc_start: 0.8348 (t80) cc_final: 0.8068 (t80)
REVERT: C   90 MET cc_start: 0.8957 (ppp) cc_final: 0.8434 (ppp)
REVERT: C   93 GLN cc_start: 0.8415 (tm-30) cc_final: 0.8071 (tm-30)
REVERT: C   94 GLU cc_start: 0.9186 (pt0) cc_final: 0.8831 (pp20)
REVERT: C  105 GLU cc_start: 0.8821 (pt0) cc_final: 0.8526 (pp20)
REVERT: C  106 ASP cc_start: 0.8582 (m-30) cc_final: 0.7897 (m-30)
REVERT: D   54 THR cc_start: 0.9287 (p) cc_final: 0.8980 (p)
REVERT: D   55 ARG cc_start: 0.9093 (mtt180) cc_final: 0.8164 (mmm-85)
REVERT: D   60 VAL cc_start: 0.9151 (p) cc_final: 0.8706 (p)
REVERT: D   78 ARG cc_start: 0.7623 (ptm-80) cc_final: 0.7380 (ptm-80)
REVERT: E   68 GLN cc_start: 0.9166 (tp40) cc_final: 0.8634 (tp40)
REVERT: E   76 GLN cc_start: 0.9027 (tt0) cc_final: 0.8445 (tp-100)
REVERT: E  110 CYS cc_start: 0.8790 (t) cc_final: 0.8401 (t)
REVERT: F   60 VAL cc_start: 0.8895 (p) cc_final: 0.8466 (p)
REVERT: F   67 ARG cc_start: 0.8974 (ttp-110) cc_final: 0.8159 (ttp-110)
REVERT: F   78 ARG cc_start: 0.7435 (ptm160) cc_final: 0.7066 (ptm160)
REVERT: F   82 THR cc_start: 0.7903 (p) cc_final: 0.7536 (p)
REVERT: G   73 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8702 (tm-30)
REVERT: G  106 ASP cc_start: 0.9032 (t70) cc_final: 0.8646 (t70)
REVERT: G  107 THR cc_start: 0.9762 (p) cc_final: 0.9505 (p)
REVERT: G  123 ASP cc_start: 0.9148 (m-30) cc_final: 0.8364 (t70)
REVERT: G  128 ARG cc_start: 0.8870 (mtp-110) cc_final: 0.8098 (mtp-110)
REVERT: H   39 ARG cc_start: 0.8697 (mmt90) cc_final: 0.8424 (mmt90)
REVERT: H   88 TYR cc_start: 0.8602 (m-10) cc_final: 0.8175 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 270
  average time/residue: 0.2908
  time to fit residues: 100.2301
Evaluate side-chains
  232 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 232
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 56 optimal weight:   20.0000
   chunk 22 optimal weight:    1.9990
   chunk 64 optimal weight:   10.0000
   chunk 67 optimal weight:   10.0000
   chunk 47 optimal weight:    0.7980
   chunk 75 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9980
   overall best weight:    2.7586

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          1.1618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  10403  Z= 0.266
  Angle     :  0.691  10.388  15068  Z= 0.399
  Chirality :  0.036   0.153   1723
  Planarity :  0.005   0.045   1069
  Dihedral  : 32.646 179.118   3286
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 17.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  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:  0.77 (0.33), residues: 578
  helix:  1.11 (0.23), residues: 457
  sheet:  None (None), residues: 0
  loop : -1.71 (0.45), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.017   0.002   PHE E  67 
 TYR   0.018   0.002   TYR B  88 
 ARG   0.016   0.001   ARG H  92 

*********************** 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
  269 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 269
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9363 (mtmt) cc_final: 0.8933 (mtmm)
REVERT: A   65 LEU cc_start: 0.9546 (tp) cc_final: 0.9193 (tp)
REVERT: A   90 MET cc_start: 0.8205 (tmm) cc_final: 0.7758 (tmm)
REVERT: A   93 GLN cc_start: 0.8990 (mt0) cc_final: 0.8152 (mt0)
REVERT: A   94 GLU cc_start: 0.8898 (pt0) cc_final: 0.8539 (pt0)
REVERT: A   97 GLU cc_start: 0.8247 (mt-10) cc_final: 0.8026 (mp0)
REVERT: A  106 ASP cc_start: 0.9327 (t70) cc_final: 0.8903 (t70)
REVERT: A  115 LYS cc_start: 0.9161 (mmmt) cc_final: 0.8930 (mmmm)
REVERT: B   24 ASP cc_start: 0.8247 (t0) cc_final: 0.7736 (t0)
REVERT: B   27 GLN cc_start: 0.8745 (mm110) cc_final: 0.8423 (mm110)
REVERT: B   63 GLU cc_start: 0.8677 (tt0) cc_final: 0.8445 (tp30)
REVERT: B   74 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7924 (tm-30)
REVERT: C   78 PHE cc_start: 0.8440 (t80) cc_final: 0.8116 (t80)
REVERT: C   90 MET cc_start: 0.8952 (ppp) cc_final: 0.8237 (ppp)
REVERT: C   94 GLU cc_start: 0.9158 (pt0) cc_final: 0.8817 (pp20)
REVERT: C  105 GLU cc_start: 0.8840 (pt0) cc_final: 0.8537 (pp20)
REVERT: C  106 ASP cc_start: 0.8549 (m-30) cc_final: 0.7894 (m-30)
REVERT: C  126 LEU cc_start: 0.9697 (tp) cc_final: 0.8765 (tt)
REVERT: D   31 LYS cc_start: 0.8935 (ttmm) cc_final: 0.8588 (ttmm)
REVERT: D   55 ARG cc_start: 0.9063 (mtt180) cc_final: 0.8420 (mmm-85)
REVERT: D   60 VAL cc_start: 0.9148 (p) cc_final: 0.8721 (p)
REVERT: D   78 ARG cc_start: 0.7569 (ptm-80) cc_final: 0.7063 (ptm-80)
REVERT: E   64 LYS cc_start: 0.8441 (mmpt) cc_final: 0.7966 (mmmt)
REVERT: E   68 GLN cc_start: 0.9242 (tp40) cc_final: 0.8723 (tp40)
REVERT: E   76 GLN cc_start: 0.9072 (tt0) cc_final: 0.8469 (tp-100)
REVERT: E   93 GLN cc_start: 0.9333 (mm110) cc_final: 0.9041 (mm110)
REVERT: E  134 ARG cc_start: 0.7693 (mmp80) cc_final: 0.7427 (mmp80)
REVERT: F   36 ARG cc_start: 0.9050 (ptt90) cc_final: 0.8818 (ptt-90)
REVERT: F   45 ARG cc_start: 0.8158 (mmm160) cc_final: 0.7790 (mmm160)
REVERT: F   60 VAL cc_start: 0.8891 (p) cc_final: 0.8425 (p)
REVERT: F   67 ARG cc_start: 0.9014 (ttp-110) cc_final: 0.8191 (ttp-110)
REVERT: F   78 ARG cc_start: 0.7488 (ptm160) cc_final: 0.7104 (ptm160)
REVERT: F   82 THR cc_start: 0.7875 (p) cc_final: 0.7528 (p)
REVERT: G  106 ASP cc_start: 0.9073 (t70) cc_final: 0.8521 (t70)
REVERT: G  128 ARG cc_start: 0.8894 (mtp-110) cc_final: 0.8139 (mtp-110)
REVERT: H   35 ARG cc_start: 0.8359 (mmt180) cc_final: 0.8019 (mmt180)
REVERT: H   88 TYR cc_start: 0.8559 (m-10) cc_final: 0.8089 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 269
  average time/residue: 0.2854
  time to fit residues: 99.0452
Evaluate side-chains
  235 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 79 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 63 optimal weight:    9.9990
   chunk 6 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 50 optimal weight:    2.9990
   chunk 67 optimal weight:   10.0000
   chunk 19 optimal weight:    7.9990
   overall best weight:    1.9588

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          1.1794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10403  Z= 0.243
  Angle     :  0.703  10.572  15068  Z= 0.401
  Chirality :  0.036   0.143   1723
  Planarity :  0.005   0.049   1069
  Dihedral  : 32.546 178.762   3286
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 17.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    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:  0.72 (0.34), residues: 578
  helix:  0.98 (0.23), residues: 459
  sheet:  None (None), residues: 0
  loop : -1.32 (0.52), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H  75 
 PHE   0.017   0.002   PHE G 104 
 TYR   0.022   0.002   TYR F  51 
 ARG   0.017   0.001   ARG H  92 

********************** 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
  271 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 271
  time to evaluate  : 0.782 
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   62 ILE cc_start: 0.8784 (tp) cc_final: 0.8464 (tt)
REVERT: A   64 LYS cc_start: 0.9324 (mtmt) cc_final: 0.8755 (mtmm)
REVERT: A   65 LEU cc_start: 0.9515 (tp) cc_final: 0.9235 (tp)
REVERT: A   90 MET cc_start: 0.8045 (tmm) cc_final: 0.7658 (tmm)
REVERT: A  106 ASP cc_start: 0.9292 (t70) cc_final: 0.8896 (t70)
REVERT: A  115 LYS cc_start: 0.9149 (mmmt) cc_final: 0.8866 (mmmm)
REVERT: B   24 ASP cc_start: 0.8291 (t0) cc_final: 0.7981 (t0)
REVERT: B   27 GLN cc_start: 0.8720 (mm110) cc_final: 0.8457 (mm110)
REVERT: B   74 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7806 (tm-30)
REVERT: C   78 PHE cc_start: 0.8439 (t80) cc_final: 0.8126 (t80)
REVERT: C   90 MET cc_start: 0.8875 (ppp) cc_final: 0.8372 (ppp)
REVERT: C   93 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7910 (tm-30)
REVERT: C   94 GLU cc_start: 0.9111 (pt0) cc_final: 0.8799 (pp20)
REVERT: C  105 GLU cc_start: 0.8840 (pt0) cc_final: 0.8517 (pp20)
REVERT: C  106 ASP cc_start: 0.8515 (m-30) cc_final: 0.7811 (m-30)
REVERT: D   31 LYS cc_start: 0.8845 (ttmm) cc_final: 0.8533 (ttmm)
REVERT: D   54 THR cc_start: 0.9286 (p) cc_final: 0.8910 (p)
REVERT: D   55 ARG cc_start: 0.8990 (mtt180) cc_final: 0.8275 (mmm-85)
REVERT: D   60 VAL cc_start: 0.9177 (p) cc_final: 0.8756 (p)
REVERT: D   84 MET cc_start: 0.8648 (mmp) cc_final: 0.8400 (ppp)
REVERT: E   64 LYS cc_start: 0.8529 (mmpt) cc_final: 0.8103 (mmmt)
REVERT: E   68 GLN cc_start: 0.9308 (tp40) cc_final: 0.8832 (tp40)
REVERT: E   76 GLN cc_start: 0.9055 (tt0) cc_final: 0.8476 (tp-100)
REVERT: E  134 ARG cc_start: 0.7729 (mmp80) cc_final: 0.7440 (mmp80)
REVERT: F   29 ILE cc_start: 0.9714 (mm) cc_final: 0.9280 (tp)
REVERT: F   45 ARG cc_start: 0.8004 (mmm160) cc_final: 0.7185 (mmm160)
REVERT: F   49 LEU cc_start: 0.9350 (tp) cc_final: 0.9108 (tp)
REVERT: F   52 GLU cc_start: 0.8799 (pm20) cc_final: 0.8359 (pm20)
REVERT: F   53 GLU cc_start: 0.8851 (pt0) cc_final: 0.8364 (pt0)
REVERT: F   60 VAL cc_start: 0.8888 (p) cc_final: 0.8375 (p)
REVERT: F   67 ARG cc_start: 0.9027 (ttp-110) cc_final: 0.8173 (ttp-110)
REVERT: F   78 ARG cc_start: 0.7566 (ptm160) cc_final: 0.7201 (ptm160)
REVERT: F   82 THR cc_start: 0.8014 (p) cc_final: 0.7516 (p)
REVERT: G   61 LEU cc_start: 0.9076 (tt) cc_final: 0.8875 (tt)
REVERT: G   97 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8183 (mt-10)
REVERT: G  106 ASP cc_start: 0.9000 (t70) cc_final: 0.8669 (t70)
REVERT: G  128 ARG cc_start: 0.8884 (mtp-110) cc_final: 0.8115 (mtp-110)
REVERT: H   39 ARG cc_start: 0.8653 (mmt90) cc_final: 0.8385 (mmt90)
REVERT: H   88 TYR cc_start: 0.8448 (m-10) cc_final: 0.7964 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 271
  average time/residue: 0.2704
  time to fit residues: 94.8807
Evaluate side-chains
  239 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 9 optimal weight:    0.0770
   chunk 17 optimal weight:    3.9990
   chunk 63 optimal weight:   10.0000
   chunk 26 optimal weight:    6.9990
   chunk 65 optimal weight:   10.0000
   chunk 8 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 55 optimal weight:    6.9990
   chunk 3 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    2.0146

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.062028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.048132 restraints weight = 57017.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.049456 restraints weight = 33593.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.050368 restraints weight = 23374.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          1.1986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10403  Z= 0.242
  Angle     :  0.692   7.967  15068  Z= 0.397
  Chirality :  0.036   0.175   1723
  Planarity :  0.005   0.054   1069
  Dihedral  : 32.512 178.249   3286
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 17.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    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:  0.69 (0.34), residues: 578
  helix:  0.97 (0.23), residues: 459
  sheet:  None (None), residues: 0
  loop : -1.36 (0.51), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS G 113 
 PHE   0.025   0.002   PHE G 104 
 TYR   0.014   0.002   TYR B  72 
 ARG   0.017   0.001   ARG H  92 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2209.47 seconds
wall clock time: 40 minutes 51.30 seconds (2451.30 seconds total)