Starting phenix.real_space_refine
on Sat Aug 23 03:18:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yoz_33991/08_2025/7yoz_33991.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yoz_33991/08_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_33991/08_2025/7yoz_33991.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yoz_33991/08_2025/7yoz_33991.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yoz_33991/08_2025/7yoz_33991.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yoz_33991/08_2025/7yoz_33991.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

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

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9752
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 619
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "B"
      Number of atoms: 594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 594
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
    Chain: "C"
      Number of atoms: 625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 625
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
    Chain: "D"
      Number of atoms: 568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 568
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 1, 'TRANS': 69}
    Chain: "E"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 619
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "F"
      Number of atoms: 565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 565
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 1, 'TRANS': 69}
    Chain: "G"
      Number of atoms: 625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 625
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
    Chain: "H"
      Number of atoms: 576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 576
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 1, 'TRANS': 70}
    Chain: "I"
      Number of atoms: 2463
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 2463
          Classifications: {'DNA': 121}
          Link IDs: {'rna3p': 120}
    Chain: "J"
      Number of atoms: 2498
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 2498
          Classifications: {'DNA': 121}
          Link IDs: {'rna3p': 120}
  Time building chain proxies: 1.96, per 1000 atoms: 0.20
  Number of scatterers: 9752
  At special positions: 0
  Unit cell: (122.85, 90.3, 113.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      20     16.00
     P     242     15.00
     O    2287      8.00
     N    1838      7.00
     C    5365      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 169.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 2 sheets defined
      79.1% alpha, 0.7% beta
      120 base pairs and 215 stacking pairs defined.
    Time for finding SS restraints: 1.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 64 through 79
      removed outlier: 3.614A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.575A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.537A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.512A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 79
    Processing helix  chain 'C' and resid 85 through 114
    Processing helix  chain 'C' and resid 120 through 131
      removed outlier: 3.526A  pdb=" N   ILE C 124 " --> pdb=" O   MET C 120 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 25 through 29
    Processing helix  chain 'D' and resid 30 through 41
    Processing helix  chain 'D' and resid 49 through 77
    Processing helix  chain 'D' and resid 82 through 95
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.531A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.563A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.537A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 63 through 79
      removed outlier: 3.653A  pdb=" N   ASP G  77 " --> pdb=" O   GLU G  73 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   PHE G  78 " --> pdb=" O   ILE G  74 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 85 through 114
    Processing helix  chain 'G' and resid 120 through 132
      removed outlier: 3.593A  pdb=" N   ILE G 124 " --> pdb=" O   MET G 120 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 24 through 29
    Processing helix  chain 'H' and resid 30 through 41
    Processing helix  chain 'H' and resid 49 through 76
    Processing helix  chain 'H' and resid 82 through 93
    Processing sheet with id=AA1, first strand: chain 'C' and resid 118 through 119
    Processing sheet with id=AA2, first strand: chain 'G' and resid 83 through 84
      removed outlier: 7.722A  pdb=" N   ARG G  83 " --> pdb=" O   VAL H  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2

    350 hydrogen bonds defined for protein.
    1023 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      313 hydrogen bonds
      626 hydrogen bond angles
      0 basepair planarities
      120 basepair parallelities
      215 stacking parallelities
  Total time for adding SS restraints: 1.32

  Time building geometry restraints manager: 0.99 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:             0.300
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     9.090
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.790
-------------------------------------------------------------------------------
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= 0.154
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.30), residues: 578
  helix:  0.94 (0.21), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.23 (0.43), residues: 128

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (10403)
  covalent geometry    : angle       0.55187 (15068)
  hydrogen bonds       : bond        0.17426 (  663)
  hydrogen bonds       : angle       4.78242 ( 1649)

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

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 335
  time to evaluate  : 0.178 
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: 0.1408
  time to fit residues: 58.2729
Evaluate side-chains
  222 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    9.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    3.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
G  68 GLN
H  75 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.079392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.064282 restraints weight = 57476.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.065808 restraints weight = 34400.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.066839 restraints weight = 24132.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.067569 restraints weight = 18736.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.068030 restraints weight = 15708.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.5440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.076  10403  Z= 0.245
  Angle     :  0.711   7.149  15068  Z= 0.409
  Chirality :  0.039   0.152   1723
  Planarity :  0.006   0.098   1069
  Dihedral  : 31.908 179.841   3286
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 17.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  4.96 %
    Favored  : 94.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.32), residues: 578
  helix:  1.52 (0.23), residues: 467
  sheet:  None (None), residues: 0
  loop : -1.30 (0.46), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG E  69 
 TYR   0.024   0.002   TYR D  72 
 PHE   0.029   0.003   PHE A 104 
 HIS   0.009   0.004   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 (10403)
  covalent geometry    : angle       0.71072 (15068)
  hydrogen bonds       : bond        0.05724 (  663)
  hydrogen bonds       : angle       3.34465 ( 1649)

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

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 260
  time to evaluate  : 0.206 
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   64 LYS cc_start: 0.9429 (mttm) cc_final: 0.9019 (mtmm)
REVERT: A   85 GLN cc_start: 0.9284 (tt0) cc_final: 0.8948 (tp40)
REVERT: A   90 MET cc_start: 0.7986 (tmm) cc_final: 0.7783 (tmm)
REVERT: A   92 LEU cc_start: 0.9712 (tt) cc_final: 0.9354 (tt)
REVERT: A   93 GLN cc_start: 0.9040 (tt0) cc_final: 0.7759 (tm-30)
REVERT: A   97 GLU cc_start: 0.8199 (tt0) cc_final: 0.7404 (mt-10)
REVERT: A  119 ILE cc_start: 0.9257 (pt) cc_final: 0.8971 (mt)
REVERT: A  123 ASP cc_start: 0.8796 (m-30) cc_final: 0.8363 (t70)
REVERT: A  130 ILE cc_start: 0.9823 (mt) cc_final: 0.9616 (mm)
REVERT: B   24 ASP cc_start: 0.8363 (t0) cc_final: 0.7804 (p0)
REVERT: B   88 TYR cc_start: 0.8758 (m-80) cc_final: 0.8532 (m-80)
REVERT: C   90 MET cc_start: 0.9155 (ppp) cc_final: 0.8645 (ppp)
REVERT: C   93 GLN cc_start: 0.9124 (tm-30) cc_final: 0.8882 (tm-30)
REVERT: C   94 GLU cc_start: 0.9265 (pt0) cc_final: 0.8916 (pt0)
REVERT: C  123 ASP cc_start: 0.9226 (m-30) cc_final: 0.8776 (m-30)
REVERT: D   49 LEU cc_start: 0.8366 (pp) cc_final: 0.8116 (pt)
REVERT: D   52 GLU cc_start: 0.9154 (tt0) cc_final: 0.8947 (pp20)
REVERT: D   55 ARG cc_start: 0.9041 (mtt180) cc_final: 0.8622 (mmm-85)
REVERT: D   59 LYS cc_start: 0.9216 (tttt) cc_final: 0.8489 (tptp)
REVERT: D   63 GLU cc_start: 0.8935 (tt0) cc_final: 0.8539 (tm-30)
REVERT: E   87 SER cc_start: 0.8866 (m) cc_final: 0.8419 (p)
REVERT: E  119 ILE cc_start: 0.8288 (pt) cc_final: 0.7935 (pt)
REVERT: E  120 MET cc_start: 0.8757 (mmp) cc_final: 0.8339 (mmm)
REVERT: E  123 ASP cc_start: 0.9067 (m-30) cc_final: 0.8801 (m-30)
REVERT: F   49 LEU cc_start: 0.9191 (tt) cc_final: 0.8540 (tt)
REVERT: F   50 ILE cc_start: 0.9486 (tp) cc_final: 0.9264 (mm)
REVERT: F   63 GLU cc_start: 0.8958 (tt0) cc_final: 0.8552 (tm-30)
REVERT: G   90 MET cc_start: 0.8690 (ttm) cc_final: 0.7963 (tmm)
REVERT: G   96 CYS cc_start: 0.8289 (m) cc_final: 0.8000 (m)
REVERT: G   97 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7863 (mt-10)
REVERT: G  123 ASP cc_start: 0.8769 (m-30) cc_final: 0.8359 (t70)
REVERT: G  126 LEU cc_start: 0.9672 (tp) cc_final: 0.9463 (tt)
REVERT: G  128 ARG cc_start: 0.9167 (mtp-110) cc_final: 0.8293 (mtp-110)
REVERT: H   35 ARG cc_start: 0.8892 (mtp85) cc_final: 0.8652 (ttm-80)
REVERT: H   74 GLU cc_start: 0.9050 (tt0) cc_final: 0.8572 (tt0)
REVERT: H   78 ARG cc_start: 0.8462 (ptp90) cc_final: 0.8172 (ptp90)
  outliers start: 3
  outliers final: 0
  residues processed: 263
  average time/residue: 0.1181
  time to fit residues: 39.2892
Evaluate side-chains
  213 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:   10.0000
   chunk 44 optimal weight:    5.9990
   chunk 78 optimal weight:   10.0000
   chunk 28 optimal weight:    7.9990
   chunk 51 optimal weight:    7.9990
   chunk 17 optimal weight:    6.9990
   chunk 76 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9990
   chunk 65 optimal weight:   10.0000
   chunk 20 optimal weight:    3.9990
   chunk 63 optimal weight:    7.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.065158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.050263 restraints weight = 60837.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.051584 restraints weight = 37055.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.052502 restraints weight = 26497.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.053105 restraints weight = 20926.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.053527 restraints weight = 17843.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.8790

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= 0.297
  Angle     :  0.746   6.972  15068  Z= 0.439
  Chirality :  0.039   0.170   1723
  Planarity :  0.007   0.106   1069
  Dihedral  : 32.514 179.965   3286
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 18.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  5.16 %
    Favored  : 94.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.33), residues: 578
  helix:  1.30 (0.23), residues: 459
  sheet:  None (None), residues: 0
  loop : -0.91 (0.48), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  45 
 TYR   0.013   0.002   TYR F  51 
 PHE   0.028   0.003   PHE G 104 
 HIS   0.011   0.003   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00658 (10403)
  covalent geometry    : angle       0.74609 (15068)
  hydrogen bonds       : bond        0.06183 (  663)
  hydrogen bonds       : angle       3.67291 ( 1649)

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

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 276
  time to evaluate  : 0.413 
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  115 LYS cc_start: 0.9188 (mmmt) cc_final: 0.8786 (mmmm)
REVERT: A  119 ILE cc_start: 0.9505 (pt) cc_final: 0.9223 (mt)
REVERT: A  128 ARG cc_start: 0.9029 (mtp180) cc_final: 0.8802 (mtp-110)
REVERT: A  130 ILE cc_start: 0.9768 (mt) cc_final: 0.9533 (tt)
REVERT: B   24 ASP cc_start: 0.8670 (t0) cc_final: 0.7861 (t0)
REVERT: B   35 ARG cc_start: 0.8418 (ttt180) cc_final: 0.7543 (ttt90)
REVERT: B   39 ARG cc_start: 0.8518 (mtm-85) cc_final: 0.8054 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8758 (tt0) cc_final: 0.8130 (tp30)
REVERT: B   68 ASP cc_start: 0.9290 (m-30) cc_final: 0.9064 (m-30)
REVERT: B   85 ASP cc_start: 0.9402 (m-30) cc_final: 0.9115 (m-30)
REVERT: B   88 TYR cc_start: 0.9048 (m-80) cc_final: 0.8731 (m-80)
REVERT: B   92 ARG cc_start: 0.8221 (ttt180) cc_final: 0.7848 (ttp80)
REVERT: C   90 MET cc_start: 0.9103 (ppp) cc_final: 0.8385 (ppp)
REVERT: C   93 GLN cc_start: 0.9180 (tm-30) cc_final: 0.8666 (tm-30)
REVERT: C  100 LEU cc_start: 0.9706 (tp) cc_final: 0.9462 (tt)
REVERT: C  123 ASP cc_start: 0.9317 (m-30) cc_final: 0.8974 (m-30)
REVERT: D   55 ARG cc_start: 0.9163 (mtt180) cc_final: 0.8821 (mtt-85)
REVERT: D   63 GLU cc_start: 0.9257 (tt0) cc_final: 0.8688 (tm-30)
REVERT: D   66 ILE cc_start: 0.9482 (mt) cc_final: 0.9234 (pt)
REVERT: E   64 LYS cc_start: 0.9140 (mmpt) cc_final: 0.8875 (mmmt)
REVERT: E   68 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8299 (tp-100)
REVERT: E   76 GLN cc_start: 0.8995 (tt0) cc_final: 0.8432 (tp-100)
REVERT: E   90 MET cc_start: 0.8630 (ppp) cc_final: 0.8383 (ppp)
REVERT: E   93 GLN cc_start: 0.9288 (mm110) cc_final: 0.8950 (tp40)
REVERT: E  119 ILE cc_start: 0.8882 (pt) cc_final: 0.8482 (pt)
REVERT: E  120 MET cc_start: 0.8717 (mmp) cc_final: 0.8476 (mmm)
REVERT: F   63 GLU cc_start: 0.9352 (tt0) cc_final: 0.9025 (tm-30)
REVERT: F   66 ILE cc_start: 0.9413 (mt) cc_final: 0.9179 (pt)
REVERT: F   84 MET cc_start: 0.8750 (ptt) cc_final: 0.8449 (ptt)
REVERT: F   88 TYR cc_start: 0.8976 (m-80) cc_final: 0.8489 (t80)
REVERT: G   60 LEU cc_start: 0.8705 (mm) cc_final: 0.8260 (mt)
REVERT: G   61 LEU cc_start: 0.9212 (tt) cc_final: 0.8665 (tt)
REVERT: G   73 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8855 (tm-30)
REVERT: G   90 MET cc_start: 0.9004 (ttm) cc_final: 0.8378 (tmm)
REVERT: G   94 GLU cc_start: 0.8867 (pt0) cc_final: 0.8595 (pt0)
REVERT: G   97 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7803 (mt-10)
REVERT: G  107 THR cc_start: 0.9753 (p) cc_final: 0.9493 (p)
REVERT: G  123 ASP cc_start: 0.8809 (m-30) cc_final: 0.8551 (t70)
REVERT: G  128 ARG cc_start: 0.9248 (mtp-110) cc_final: 0.9023 (mtp-110)
REVERT: H   35 ARG cc_start: 0.9195 (mtp85) cc_final: 0.8880 (ttm-80)
REVERT: H   63 GLU cc_start: 0.8458 (tt0) cc_final: 0.8220 (tt0)
REVERT: H   67 ARG cc_start: 0.9234 (ttm170) cc_final: 0.8943 (ttm110)
REVERT: H   78 ARG cc_start: 0.8906 (ptp90) cc_final: 0.8697 (ptp90)
REVERT: H   88 TYR cc_start: 0.8791 (m-10) cc_final: 0.8417 (m-10)
  outliers start: 2
  outliers final: 1
  residues processed: 278
  average time/residue: 0.1147
  time to fit residues: 41.1079
Evaluate side-chains
  232 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 231
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 57 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 67 optimal weight:   10.0000
   chunk 61 optimal weight:   10.0000
   chunk 78 optimal weight:   10.0000
   chunk 70 optimal weight:   10.0000
   chunk 62 optimal weight:   10.0000
   chunk 64 optimal weight:   10.0000
   overall best weight:    5.9992

-------------------------------------------------------------------------------
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  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
** G  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.059725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.045166 restraints weight = 60753.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.046379 restraints weight = 37168.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.047198 restraints weight = 26897.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.047678 restraints weight = 21566.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.048069 restraints weight = 18869.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          1.0388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.055  10403  Z= 0.314
  Angle     :  0.747   7.483  15068  Z= 0.443
  Chirality :  0.041   0.178   1723
  Planarity :  0.006   0.049   1069
  Dihedral  : 33.212 179.956   3286
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 19.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  5.36 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.32), residues: 578
  helix:  0.90 (0.23), residues: 461
  sheet:  None (None), residues: 0
  loop : -1.55 (0.43), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A  72 
 TYR   0.013   0.002   TYR F  51 
 PHE   0.015   0.002   PHE C 104 
 HIS   0.009   0.003   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00699 (10403)
  covalent geometry    : angle       0.74718 (15068)
  hydrogen bonds       : bond        0.06703 (  663)
  hydrogen bonds       : angle       3.65446 ( 1649)

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

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 266
  time to evaluate  : 0.249 
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: 0.9175 (tt) cc_final: 0.8773 (tt)
REVERT: A   64 LYS cc_start: 0.9402 (mtmt) cc_final: 0.9037 (mtmm)
REVERT: A   68 GLN cc_start: 0.9490 (tt0) cc_final: 0.9099 (tp-100)
REVERT: A   85 GLN cc_start: 0.9296 (tt0) cc_final: 0.8899 (tp40)
REVERT: A   90 MET cc_start: 0.8267 (tmm) cc_final: 0.8057 (tmm)
REVERT: A   94 GLU cc_start: 0.9012 (pt0) cc_final: 0.8616 (pt0)
REVERT: A   97 GLU cc_start: 0.8767 (mt-10) cc_final: 0.7713 (mt-10)
REVERT: A  106 ASP cc_start: 0.9178 (t70) cc_final: 0.8599 (t70)
REVERT: A  115 LYS cc_start: 0.9183 (mmmt) cc_final: 0.8836 (mmmm)
REVERT: B   25 ASN cc_start: 0.7949 (t0) cc_final: 0.7748 (t0)
REVERT: B   88 TYR cc_start: 0.8817 (m-80) cc_final: 0.8188 (m-10)
REVERT: C   90 MET cc_start: 0.8931 (ppp) cc_final: 0.8204 (ppp)
REVERT: C   94 GLU cc_start: 0.9239 (pt0) cc_final: 0.8677 (pt0)
REVERT: C  123 ASP cc_start: 0.9207 (m-30) cc_final: 0.9003 (m-30)
REVERT: D   49 LEU cc_start: 0.8476 (pp) cc_final: 0.8245 (pt)
REVERT: D   55 ARG cc_start: 0.9135 (mtt180) cc_final: 0.8461 (mmm-85)
REVERT: D   63 GLU cc_start: 0.9200 (tt0) cc_final: 0.8857 (tm-30)
REVERT: D   78 ARG cc_start: 0.7957 (ptm-80) cc_final: 0.7745 (ptm-80)
REVERT: E   76 GLN cc_start: 0.8979 (tt0) cc_final: 0.8431 (tp-100)
REVERT: E   93 GLN cc_start: 0.9240 (mm110) cc_final: 0.8828 (tp40)
REVERT: E  119 ILE cc_start: 0.8887 (pt) cc_final: 0.8409 (pt)
REVERT: E  120 MET cc_start: 0.8813 (mmp) cc_final: 0.8275 (mmm)
REVERT: E  123 ASP cc_start: 0.9137 (m-30) cc_final: 0.8799 (m-30)
REVERT: E  134 ARG cc_start: 0.8044 (mmm160) cc_final: 0.7819 (mmm160)
REVERT: F   63 GLU cc_start: 0.9351 (tt0) cc_final: 0.8966 (tm-30)
REVERT: F   84 MET cc_start: 0.8750 (ptt) cc_final: 0.8513 (ptt)
REVERT: F   88 TYR cc_start: 0.8862 (m-80) cc_final: 0.8550 (t80)
REVERT: G   73 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8814 (tm-30)
REVERT: G   90 MET cc_start: 0.8930 (ttm) cc_final: 0.8449 (tmm)
REVERT: G  107 THR cc_start: 0.9756 (p) cc_final: 0.9314 (p)
REVERT: G  123 ASP cc_start: 0.8757 (m-30) cc_final: 0.8425 (t70)
REVERT: G  128 ARG cc_start: 0.9110 (mtp-110) cc_final: 0.8284 (mtp-110)
REVERT: H   35 ARG cc_start: 0.9213 (mtp85) cc_final: 0.8850 (ttm110)
REVERT: H   67 ARG cc_start: 0.9082 (ttm170) cc_final: 0.8880 (ttm110)
REVERT: H   74 GLU cc_start: 0.9037 (tt0) cc_final: 0.8662 (tt0)
REVERT: H   85 ASP cc_start: 0.9167 (m-30) cc_final: 0.8955 (m-30)
REVERT: H   88 TYR cc_start: 0.8796 (m-10) cc_final: 0.8494 (m-10)
  outliers start: 3
  outliers final: 1
  residues processed: 268
  average time/residue: 0.1058
  time to fit residues: 36.9721
Evaluate side-chains
  221 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 220
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
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 39 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 76 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   chunk 69 optimal weight:   10.0000
   chunk 54 optimal weight:    0.8980
   chunk 27 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 57 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   overall best weight:    3.3788

-------------------------------------------------------------------------------
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  93 GLN
C  85 GLN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.060614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.046365 restraints weight = 60033.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.047615 restraints weight = 36140.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.048434 restraints weight = 25720.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.049017 restraints weight = 20454.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.049365 restraints weight = 17490.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          1.0830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  10403  Z= 0.224
  Angle     :  0.699  13.158  15068  Z= 0.407
  Chirality :  0.037   0.199   1723
  Planarity :  0.005   0.066   1069
  Dihedral  : 33.086 178.886   3286
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 17.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.32), residues: 578
  helix:  1.17 (0.23), residues: 457
  sheet:  None (None), residues: 0
  loop : -1.45 (0.42), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 129 
 TYR   0.013   0.001   TYR D  72 
 PHE   0.017   0.002   PHE G 104 
 HIS   0.008   0.002   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 (10403)
  covalent geometry    : angle       0.69892 (15068)
  hydrogen bonds       : bond        0.04959 (  663)
  hydrogen bonds       : angle       3.38859 ( 1649)

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

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 289
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: 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: 0.9202 (mt) cc_final: 0.8948 (mt)
REVERT: A   61 LEU cc_start: 0.9038 (tt) cc_final: 0.8689 (tt)
REVERT: A   64 LYS cc_start: 0.9379 (mtmt) cc_final: 0.9012 (mtmm)
REVERT: A   65 LEU cc_start: 0.9644 (tp) cc_final: 0.9396 (tp)
REVERT: A   94 GLU cc_start: 0.8906 (pt0) cc_final: 0.8549 (pt0)
REVERT: A   97 GLU cc_start: 0.8772 (mt-10) cc_final: 0.7682 (mt-10)
REVERT: A  106 ASP cc_start: 0.9146 (t70) cc_final: 0.8604 (t70)
REVERT: A  109 LEU cc_start: 0.9228 (tt) cc_final: 0.8968 (tt)
REVERT: A  115 LYS cc_start: 0.9217 (mmmt) cc_final: 0.8899 (mmmm)
REVERT: B   24 ASP cc_start: 0.8455 (t0) cc_final: 0.7844 (t0)
REVERT: B   25 ASN cc_start: 0.8036 (t0) cc_final: 0.7727 (t0)
REVERT: B   27 GLN cc_start: 0.8775 (mm110) cc_final: 0.8513 (mm110)
REVERT: B   63 GLU cc_start: 0.8725 (tt0) cc_final: 0.8216 (tp30)
REVERT: B   85 ASP cc_start: 0.9304 (m-30) cc_final: 0.9043 (m-30)
REVERT: C   90 MET cc_start: 0.8911 (ppp) cc_final: 0.8312 (ppp)
REVERT: C  123 ASP cc_start: 0.9242 (m-30) cc_final: 0.8966 (m-30)
REVERT: D   55 ARG cc_start: 0.9126 (mtt180) cc_final: 0.8561 (mmm-85)
REVERT: D   63 GLU cc_start: 0.9159 (tt0) cc_final: 0.8958 (tm-30)
REVERT: D   64 ASN cc_start: 0.9226 (t0) cc_final: 0.8952 (m-40)
REVERT: E   64 LYS cc_start: 0.8858 (mmpt) cc_final: 0.8384 (mmmt)
REVERT: E   76 GLN cc_start: 0.8982 (tt0) cc_final: 0.8423 (tp-100)
REVERT: E  110 CYS cc_start: 0.8824 (t) cc_final: 0.8484 (t)
REVERT: E  119 ILE cc_start: 0.8940 (pt) cc_final: 0.8668 (pt)
REVERT: E  123 ASP cc_start: 0.9121 (m-30) cc_final: 0.8650 (m-30)
REVERT: F   29 ILE cc_start: 0.9580 (mm) cc_final: 0.9210 (mm)
REVERT: F   54 THR cc_start: 0.9218 (p) cc_final: 0.8981 (p)
REVERT: F   63 GLU cc_start: 0.9442 (tt0) cc_final: 0.8967 (tm-30)
REVERT: F   78 ARG cc_start: 0.7715 (ptm160) cc_final: 0.7361 (ptm160)
REVERT: F   82 THR cc_start: 0.7924 (p) cc_final: 0.7679 (p)
REVERT: F   84 MET cc_start: 0.8682 (ptt) cc_final: 0.8452 (ptt)
REVERT: F   88 TYR cc_start: 0.8777 (m-80) cc_final: 0.8456 (t80)
REVERT: G   61 LEU cc_start: 0.9067 (tt) cc_final: 0.8835 (tt)
REVERT: G   73 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8771 (tm-30)
REVERT: G   90 MET cc_start: 0.8898 (ttm) cc_final: 0.8353 (tmm)
REVERT: G   94 GLU cc_start: 0.8777 (pt0) cc_final: 0.8572 (pt0)
REVERT: G  107 THR cc_start: 0.9771 (p) cc_final: 0.9288 (p)
REVERT: G  123 ASP cc_start: 0.8856 (m-30) cc_final: 0.8313 (t70)
REVERT: G  128 ARG cc_start: 0.9033 (mtp-110) cc_final: 0.8155 (mtp-110)
REVERT: H   35 ARG cc_start: 0.9233 (mtp85) cc_final: 0.8905 (ttm110)
REVERT: H   88 TYR cc_start: 0.8652 (m-10) cc_final: 0.8212 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 289
  average time/residue: 0.1296
  time to fit residues: 47.4052
Evaluate side-chains
  241 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 35 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   chunk 79 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 4 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   chunk 61 optimal weight:   10.0000
   chunk 46 optimal weight:    2.9990
   overall best weight:    2.9786

-------------------------------------------------------------------------------
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**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.060272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.046288 restraints weight = 58999.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.047544 restraints weight = 35059.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.048380 restraints weight = 24754.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.048974 restraints weight = 19535.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.049347 restraints weight = 16602.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          1.1206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  10403  Z= 0.211
  Angle     :  0.680   9.565  15068  Z= 0.401
  Chirality :  0.036   0.146   1723
  Planarity :  0.004   0.034   1069
  Dihedral  : 33.056 179.963   3286
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 17.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.33), residues: 578
  helix:  1.28 (0.23), residues: 455
  sheet:  None (None), residues: 0
  loop : -1.64 (0.43), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 128 
 TYR   0.015   0.002   TYR D  72 
 PHE   0.022   0.002   PHE E  67 
 HIS   0.007   0.002   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 (10403)
  covalent geometry    : angle       0.68047 (15068)
  hydrogen bonds       : bond        0.04724 (  663)
  hydrogen bonds       : angle       3.28741 ( 1649)

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

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 283
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.9075 (mt) cc_final: 0.8761 (mt)
REVERT: A   61 LEU cc_start: 0.8955 (tt) cc_final: 0.8664 (tt)
REVERT: A   64 LYS cc_start: 0.9472 (mtmt) cc_final: 0.9039 (mtmm)
REVERT: A   65 LEU cc_start: 0.9638 (tp) cc_final: 0.9382 (tp)
REVERT: A   93 GLN cc_start: 0.9076 (mt0) cc_final: 0.8723 (mt0)
REVERT: A   94 GLU cc_start: 0.8923 (pt0) cc_final: 0.8446 (pt0)
REVERT: A   97 GLU cc_start: 0.8575 (mt-10) cc_final: 0.7377 (mt-10)
REVERT: A  106 ASP cc_start: 0.9055 (t70) cc_final: 0.8433 (t70)
REVERT: A  109 LEU cc_start: 0.9107 (tt) cc_final: 0.8883 (tt)
REVERT: A  115 LYS cc_start: 0.9097 (mmmt) cc_final: 0.8868 (mmmm)
REVERT: A  130 ILE cc_start: 0.9632 (mm) cc_final: 0.9417 (mm)
REVERT: B   24 ASP cc_start: 0.8343 (t0) cc_final: 0.7717 (t0)
REVERT: B   25 ASN cc_start: 0.8034 (t0) cc_final: 0.7826 (t0)
REVERT: B   63 GLU cc_start: 0.8626 (tt0) cc_final: 0.8213 (tp30)
REVERT: B   74 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7917 (tm-30)
REVERT: C   83 ARG cc_start: 0.6733 (mtt-85) cc_final: 0.6468 (mtt180)
REVERT: C   90 MET cc_start: 0.8740 (ppp) cc_final: 0.8062 (ppp)
REVERT: C   94 GLU cc_start: 0.9188 (pt0) cc_final: 0.8638 (pt0)
REVERT: C  123 ASP cc_start: 0.9268 (m-30) cc_final: 0.8997 (m-30)
REVERT: D   55 ARG cc_start: 0.9023 (mtt180) cc_final: 0.8368 (mmm-85)
REVERT: D   64 ASN cc_start: 0.9273 (t0) cc_final: 0.8980 (m-40)
REVERT: E   68 GLN cc_start: 0.9083 (tp40) cc_final: 0.8703 (tp40)
REVERT: E   76 GLN cc_start: 0.8934 (tt0) cc_final: 0.8438 (tp-100)
REVERT: E  123 ASP cc_start: 0.9081 (m-30) cc_final: 0.8804 (m-30)
REVERT: F   63 GLU cc_start: 0.9395 (tt0) cc_final: 0.8886 (tm-30)
REVERT: F   78 ARG cc_start: 0.7996 (ptm160) cc_final: 0.7612 (ptm160)
REVERT: F   82 THR cc_start: 0.8127 (p) cc_final: 0.7759 (p)
REVERT: F   88 TYR cc_start: 0.8687 (m-80) cc_final: 0.8487 (t80)
REVERT: G   73 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8750 (tm-30)
REVERT: G   80 THR cc_start: 0.8556 (p) cc_final: 0.8118 (p)
REVERT: G   97 GLU cc_start: 0.8064 (mp0) cc_final: 0.7244 (mt-10)
REVERT: G  123 ASP cc_start: 0.8879 (m-30) cc_final: 0.8640 (m-30)
REVERT: G  128 ARG cc_start: 0.9038 (mtp-110) cc_final: 0.8196 (mtp-110)
REVERT: H   35 ARG cc_start: 0.9142 (mtp85) cc_final: 0.8237 (ttm110)
REVERT: H   39 ARG cc_start: 0.8600 (mpt-90) cc_final: 0.8392 (mpt-90)
REVERT: H   85 ASP cc_start: 0.9086 (m-30) cc_final: 0.8875 (m-30)
REVERT: H   88 TYR cc_start: 0.8209 (m-10) cc_final: 0.7756 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 283
  average time/residue: 0.1406
  time to fit residues: 50.8330
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  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 29 optimal weight:   10.0000
   chunk 68 optimal weight:   20.0000
   chunk 15 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 70 optimal weight:   10.0000
   chunk 53 optimal weight:    0.7980
   chunk 58 optimal weight:   10.0000
   chunk 59 optimal weight:   10.0000
   chunk 20 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   overall best weight:    1.5782

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.062077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.047772 restraints weight = 58785.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.049077 restraints weight = 35280.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.049948 restraints weight = 25015.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.050513 restraints weight = 19718.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.050912 restraints weight = 16860.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          1.1322

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= 0.177
  Angle     :  0.676  10.723  15068  Z= 0.391
  Chirality :  0.036   0.152   1723
  Planarity :  0.005   0.058   1069
  Dihedral  : 32.858 179.892   3286
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 15.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (0.33), residues: 578
  helix:  1.11 (0.23), residues: 464
  sheet:  None (None), residues: 0
  loop : -1.77 (0.47), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  72 
 TYR   0.012   0.001   TYR D  72 
 PHE   0.022   0.002   PHE G 104 
 HIS   0.006   0.002   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (10403)
  covalent geometry    : angle       0.67599 (15068)
  hydrogen bonds       : bond        0.04126 (  663)
  hydrogen bonds       : angle       3.21683 ( 1649)

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

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 294
  time to evaluate  : 0.260 
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: 0.8819 (tt) cc_final: 0.8523 (tt)
REVERT: A   64 LYS cc_start: 0.9497 (mtmt) cc_final: 0.9097 (mtmm)
REVERT: A   65 LEU cc_start: 0.9625 (tp) cc_final: 0.9314 (tp)
REVERT: A   93 GLN cc_start: 0.9099 (mt0) cc_final: 0.8850 (mt0)
REVERT: A   94 GLU cc_start: 0.8919 (pt0) cc_final: 0.8546 (pt0)
REVERT: A   97 GLU cc_start: 0.8548 (mt-10) cc_final: 0.7423 (mt-10)
REVERT: A  106 ASP cc_start: 0.9020 (t70) cc_final: 0.8559 (t70)
REVERT: A  115 LYS cc_start: 0.9120 (mmmt) cc_final: 0.8865 (mmmm)
REVERT: A  125 GLN cc_start: 0.9070 (tp40) cc_final: 0.8840 (mm-40)
REVERT: B   24 ASP cc_start: 0.8707 (t0) cc_final: 0.8489 (t0)
REVERT: B   29 ILE cc_start: 0.9666 (pt) cc_final: 0.9371 (mt)
REVERT: B   35 ARG cc_start: 0.8481 (ttt90) cc_final: 0.8178 (ttt180)
REVERT: B   59 LYS cc_start: 0.9331 (tptm) cc_final: 0.9104 (tptm)
REVERT: B   63 GLU cc_start: 0.8610 (tt0) cc_final: 0.8144 (tp30)
REVERT: C   90 MET cc_start: 0.8620 (ppp) cc_final: 0.8269 (ppp)
REVERT: C   94 GLU cc_start: 0.9155 (pt0) cc_final: 0.8863 (pt0)
REVERT: C  101 VAL cc_start: 0.9457 (p) cc_final: 0.9004 (p)
REVERT: C  105 GLU cc_start: 0.8820 (pm20) cc_final: 0.8566 (pm20)
REVERT: C  123 ASP cc_start: 0.9221 (m-30) cc_final: 0.8953 (m-30)
REVERT: D   55 ARG cc_start: 0.8940 (mtt180) cc_final: 0.8401 (mtt90)
REVERT: D   67 ARG cc_start: 0.9176 (mtp-110) cc_final: 0.8948 (mtm110)
REVERT: E   68 GLN cc_start: 0.9106 (tp40) cc_final: 0.8730 (tp40)
REVERT: E   76 GLN cc_start: 0.8946 (tt0) cc_final: 0.8403 (tp-100)
REVERT: E  103 LEU cc_start: 0.9215 (tt) cc_final: 0.8895 (pp)
REVERT: E  110 CYS cc_start: 0.8783 (t) cc_final: 0.8173 (t)
REVERT: E  123 ASP cc_start: 0.8931 (m-30) cc_final: 0.8593 (m-30)
REVERT: F   52 GLU cc_start: 0.8534 (pm20) cc_final: 0.8167 (pm20)
REVERT: F   63 GLU cc_start: 0.9412 (tt0) cc_final: 0.8810 (tm-30)
REVERT: F   64 ASN cc_start: 0.9175 (m-40) cc_final: 0.8426 (m-40)
REVERT: F   67 ARG cc_start: 0.9196 (ttp80) cc_final: 0.8304 (ttp-110)
REVERT: F   78 ARG cc_start: 0.8029 (ptm160) cc_final: 0.7658 (ptm160)
REVERT: F   82 THR cc_start: 0.8198 (p) cc_final: 0.7802 (p)
REVERT: F   88 TYR cc_start: 0.8760 (m-80) cc_final: 0.8478 (t80)
REVERT: G   73 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8767 (tm-30)
REVERT: G   80 THR cc_start: 0.8585 (p) cc_final: 0.8092 (p)
REVERT: G   92 LEU cc_start: 0.9712 (mm) cc_final: 0.9217 (mm)
REVERT: G   96 CYS cc_start: 0.8371 (m) cc_final: 0.8143 (m)
REVERT: G   97 GLU cc_start: 0.7626 (mp0) cc_final: 0.7411 (mt-10)
REVERT: G  123 ASP cc_start: 0.8886 (m-30) cc_final: 0.8596 (m-30)
REVERT: G  128 ARG cc_start: 0.8925 (mtp-110) cc_final: 0.8171 (mtp-110)
REVERT: H   25 ASN cc_start: 0.9219 (p0) cc_final: 0.8758 (p0)
REVERT: H   35 ARG cc_start: 0.9173 (mtp85) cc_final: 0.8211 (ttm110)
REVERT: H   39 ARG cc_start: 0.8618 (mpt-90) cc_final: 0.8392 (mpt-90)
REVERT: H   68 ASP cc_start: 0.8651 (m-30) cc_final: 0.8158 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 294
  average time/residue: 0.1358
  time to fit residues: 51.6276
Evaluate side-chains
  248 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 56 optimal weight:   20.0000
   chunk 40 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 57 optimal weight:   10.0000
   chunk 50 optimal weight:    7.9990
   chunk 74 optimal weight:   10.0000
   chunk 42 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9980
   chunk 29 optimal weight:   10.0000
   overall best weight:    1.5782

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.062454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.048370 restraints weight = 59067.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.049677 restraints weight = 35381.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.050574 restraints weight = 25010.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.051191 restraints weight = 19622.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.051589 restraints weight = 16585.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          1.1559

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= 0.174
  Angle     :  0.682  10.341  15068  Z= 0.392
  Chirality :  0.036   0.223   1723
  Planarity :  0.005   0.046   1069
  Dihedral  : 32.706 178.899   3286
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 16.47
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.33), residues: 578
  helix:  1.06 (0.23), residues: 461
  sheet:  None (None), residues: 0
  loop : -1.57 (0.50), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG H  92 
 TYR   0.013   0.001   TYR D  72 
 PHE   0.023   0.002   PHE G 104 
 HIS   0.005   0.002   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (10403)
  covalent geometry    : angle       0.68180 (15068)
  hydrogen bonds       : bond        0.04087 (  663)
  hydrogen bonds       : angle       3.19894 ( 1649)

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

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 280
  time to evaluate  : 0.309 
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: 0.8723 (tt) cc_final: 0.8521 (tt)
REVERT: A   64 LYS cc_start: 0.9516 (mtmt) cc_final: 0.9109 (mtmm)
REVERT: A   65 LEU cc_start: 0.9641 (tp) cc_final: 0.9296 (tp)
REVERT: A   93 GLN cc_start: 0.9101 (mt0) cc_final: 0.8756 (tt0)
REVERT: A   94 GLU cc_start: 0.8936 (pt0) cc_final: 0.8637 (pt0)
REVERT: A   97 GLU cc_start: 0.8538 (mt-10) cc_final: 0.7473 (mt-10)
REVERT: A  106 ASP cc_start: 0.8966 (t70) cc_final: 0.8656 (t70)
REVERT: B   24 ASP cc_start: 0.8797 (t0) cc_final: 0.8525 (t0)
REVERT: B   25 ASN cc_start: 0.7305 (t0) cc_final: 0.6958 (t0)
REVERT: B   26 ILE cc_start: 0.7895 (tp) cc_final: 0.7151 (tp)
REVERT: B   29 ILE cc_start: 0.9677 (pt) cc_final: 0.9383 (mt)
REVERT: B   59 LYS cc_start: 0.9317 (tptm) cc_final: 0.9101 (tptm)
REVERT: C   86 SER cc_start: 0.8456 (t) cc_final: 0.7554 (t)
REVERT: C   97 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8553 (mm-30)
REVERT: C  105 GLU cc_start: 0.8787 (pm20) cc_final: 0.8572 (pm20)
REVERT: D   55 ARG cc_start: 0.8989 (mtt180) cc_final: 0.8323 (mmm-85)
REVERT: D   63 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8491 (tm-30)
REVERT: D   67 ARG cc_start: 0.9212 (mtp-110) cc_final: 0.8833 (mtm110)
REVERT: E   68 GLN cc_start: 0.9109 (tp40) cc_final: 0.8720 (tp-100)
REVERT: E   76 GLN cc_start: 0.8936 (tt0) cc_final: 0.8415 (tp-100)
REVERT: E  110 CYS cc_start: 0.8612 (t) cc_final: 0.8024 (t)
REVERT: E  123 ASP cc_start: 0.8876 (m-30) cc_final: 0.8586 (m-30)
REVERT: F   52 GLU cc_start: 0.8522 (pm20) cc_final: 0.8277 (pm20)
REVERT: F   54 THR cc_start: 0.9351 (p) cc_final: 0.9083 (p)
REVERT: F   63 GLU cc_start: 0.9412 (tt0) cc_final: 0.8819 (tm-30)
REVERT: F   64 ASN cc_start: 0.9168 (m-40) cc_final: 0.8405 (m-40)
REVERT: F   67 ARG cc_start: 0.9202 (ttp80) cc_final: 0.8355 (ttp-110)
REVERT: F   78 ARG cc_start: 0.8086 (ptm160) cc_final: 0.7756 (ptm160)
REVERT: F   82 THR cc_start: 0.8196 (p) cc_final: 0.7746 (p)
REVERT: F   88 TYR cc_start: 0.8794 (m-80) cc_final: 0.8513 (t80)
REVERT: G   73 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8710 (tm-30)
REVERT: G   76 GLN cc_start: 0.9093 (tp-100) cc_final: 0.8884 (tp-100)
REVERT: G   92 LEU cc_start: 0.9691 (mm) cc_final: 0.9282 (mm)
REVERT: G  106 ASP cc_start: 0.9271 (t0) cc_final: 0.8946 (t0)
REVERT: G  123 ASP cc_start: 0.8918 (m-30) cc_final: 0.8623 (m-30)
REVERT: G  128 ARG cc_start: 0.8923 (mtp-110) cc_final: 0.8192 (mtp-110)
REVERT: H   35 ARG cc_start: 0.9132 (mtp85) cc_final: 0.8088 (ttm110)
REVERT: H   39 ARG cc_start: 0.8589 (mpt-90) cc_final: 0.8372 (mpt-90)
REVERT: H   52 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8656 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 280
  average time/residue: 0.1419
  time to fit residues: 50.6932
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  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 62 optimal weight:    9.9990
   chunk 72 optimal weight:   10.0000
   chunk 44 optimal weight:    1.9990
   chunk 27 optimal weight:   10.0000
   chunk 11 optimal weight:    0.5980
   chunk 31 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    1.9990
   chunk 77 optimal weight:   10.0000
   chunk 24 optimal weight:    3.9990
   overall best weight:    2.9188

-------------------------------------------------------------------------------
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**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.060422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.046373 restraints weight = 60767.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.047676 restraints weight = 36061.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.048561 restraints weight = 25384.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.049153 restraints weight = 19914.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.049496 restraints weight = 16829.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          1.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080  10403  Z= 0.209
  Angle     :  0.701   8.974  15068  Z= 0.406
  Chirality :  0.037   0.187   1723
  Planarity :  0.005   0.074   1069
  Dihedral  : 32.820 178.455   3286
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 18.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.33), residues: 578
  helix:  0.85 (0.23), residues: 465
  sheet:  None (None), residues: 0
  loop : -1.86 (0.46), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  39 
 TYR   0.020   0.002   TYR B  72 
 PHE   0.025   0.002   PHE G 104 
 HIS   0.007   0.002   HIS G 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 (10403)
  covalent geometry    : angle       0.70130 (15068)
  hydrogen bonds       : bond        0.04679 (  663)
  hydrogen bonds       : angle       3.40483 ( 1649)

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

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 271
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 LEU cc_start: 0.8784 (tt) cc_final: 0.8569 (tt)
REVERT: A   64 LYS cc_start: 0.9532 (mtmt) cc_final: 0.9127 (mtmm)
REVERT: A   65 LEU cc_start: 0.9566 (tp) cc_final: 0.9174 (tp)
REVERT: A   76 GLN cc_start: 0.8989 (tm-30) cc_final: 0.8709 (tp-100)
REVERT: A   93 GLN cc_start: 0.9208 (mt0) cc_final: 0.8223 (mt0)
REVERT: A   94 GLU cc_start: 0.8958 (pt0) cc_final: 0.8591 (pt0)
REVERT: A   97 GLU cc_start: 0.8629 (mt-10) cc_final: 0.7487 (mt-10)
REVERT: A  106 ASP cc_start: 0.9093 (t70) cc_final: 0.8755 (t70)
REVERT: B   24 ASP cc_start: 0.8870 (t0) cc_final: 0.8510 (t0)
REVERT: B   25 ASN cc_start: 0.7464 (t0) cc_final: 0.6962 (t0)
REVERT: B   26 ILE cc_start: 0.8147 (tp) cc_final: 0.6831 (tp)
REVERT: B   27 GLN cc_start: 0.8959 (mp10) cc_final: 0.8558 (mp10)
REVERT: B   59 LYS cc_start: 0.9336 (tptm) cc_final: 0.9112 (tptm)
REVERT: B   63 GLU cc_start: 0.8616 (tt0) cc_final: 0.8128 (tp30)
REVERT: B   74 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8106 (tm-30)
REVERT: C   86 SER cc_start: 0.8091 (t) cc_final: 0.7597 (t)
REVERT: C   90 MET cc_start: 0.8779 (ptp) cc_final: 0.8443 (ptt)
REVERT: C  105 GLU cc_start: 0.8745 (pm20) cc_final: 0.8431 (pm20)
REVERT: C  129 ARG cc_start: 0.9188 (mtp-110) cc_final: 0.8859 (ttp-110)
REVERT: D   35 ARG cc_start: 0.8898 (mtp-110) cc_final: 0.8593 (ttm110)
REVERT: D   44 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8669 (mmmm)
REVERT: D   55 ARG cc_start: 0.9035 (mtt180) cc_final: 0.8334 (mmm-85)
REVERT: D   63 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8485 (tm-30)
REVERT: D   67 ARG cc_start: 0.9193 (mtp-110) cc_final: 0.8727 (mtm110)
REVERT: E   68 GLN cc_start: 0.9174 (tp40) cc_final: 0.8750 (tp-100)
REVERT: E   76 GLN cc_start: 0.8980 (tt0) cc_final: 0.8503 (tp-100)
REVERT: E   93 GLN cc_start: 0.9333 (mm110) cc_final: 0.8982 (mm110)
REVERT: E  110 CYS cc_start: 0.8605 (t) cc_final: 0.8004 (t)
REVERT: E  123 ASP cc_start: 0.8879 (m-30) cc_final: 0.8502 (m-30)
REVERT: F   29 ILE cc_start: 0.9603 (mm) cc_final: 0.9279 (mm)
REVERT: F   55 ARG cc_start: 0.8960 (mmt90) cc_final: 0.8742 (mmt90)
REVERT: F   63 GLU cc_start: 0.9418 (tt0) cc_final: 0.8796 (tm-30)
REVERT: F   64 ASN cc_start: 0.9181 (m-40) cc_final: 0.8357 (m-40)
REVERT: F   67 ARG cc_start: 0.9198 (ttp80) cc_final: 0.8217 (ttp-110)
REVERT: F   78 ARG cc_start: 0.8132 (ptm160) cc_final: 0.7768 (ptm160)
REVERT: F   82 THR cc_start: 0.8277 (p) cc_final: 0.7863 (p)
REVERT: F   88 TYR cc_start: 0.8809 (m-80) cc_final: 0.8508 (t80)
REVERT: G   73 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8767 (tm-30)
REVERT: G   80 THR cc_start: 0.8660 (p) cc_final: 0.8207 (p)
REVERT: G   93 GLN cc_start: 0.9381 (mm110) cc_final: 0.9001 (mm-40)
REVERT: G   97 GLU cc_start: 0.8100 (mp0) cc_final: 0.7671 (mp0)
REVERT: G  106 ASP cc_start: 0.9092 (t0) cc_final: 0.8874 (t70)
REVERT: G  123 ASP cc_start: 0.9061 (m-30) cc_final: 0.8774 (m-30)
REVERT: G  128 ARG cc_start: 0.8951 (mtp-110) cc_final: 0.8107 (mtp-110)
REVERT: H   35 ARG cc_start: 0.9138 (mtp85) cc_final: 0.8161 (ttm110)
REVERT: H   74 GLU cc_start: 0.8951 (tt0) cc_final: 0.8580 (tt0)
REVERT: H   88 TYR cc_start: 0.8471 (m-10) cc_final: 0.8061 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 271
  average time/residue: 0.1306
  time to fit residues: 46.0087
Evaluate side-chains
  231 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 33 optimal weight:    7.9990
   chunk 75 optimal weight:   10.0000
   chunk 78 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.062813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.049133 restraints weight = 58675.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.050417 restraints weight = 35150.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.051288 restraints weight = 24720.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.051875 restraints weight = 19388.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.052261 restraints weight = 16424.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          1.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10403  Z= 0.167
  Angle     :  0.689   9.571  15068  Z= 0.392
  Chirality :  0.037   0.210   1723
  Planarity :  0.005   0.055   1069
  Dihedral  : 32.558 178.682   3286
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 15.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.33), residues: 578
  helix:  0.87 (0.23), residues: 465
  sheet:  None (None), residues: 0
  loop : -1.33 (0.53), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG H  92 
 TYR   0.011   0.001   TYR B  88 
 PHE   0.020   0.002   PHE G 104 
 HIS   0.005   0.002   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (10403)
  covalent geometry    : angle       0.68909 (15068)
  hydrogen bonds       : bond        0.03909 (  663)
  hydrogen bonds       : angle       3.17973 ( 1649)

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

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 276
  time to evaluate  : 0.188 
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   61 LEU cc_start: 0.8618 (tt) cc_final: 0.8382 (tt)
REVERT: A   64 LYS cc_start: 0.9493 (mtmt) cc_final: 0.9115 (mtmm)
REVERT: A   65 LEU cc_start: 0.9545 (tp) cc_final: 0.9181 (tp)
REVERT: A   76 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8522 (tp-100)
REVERT: A   93 GLN cc_start: 0.9006 (mt0) cc_final: 0.8676 (mt0)
REVERT: A   94 GLU cc_start: 0.8900 (pt0) cc_final: 0.8568 (pt0)
REVERT: A   97 GLU cc_start: 0.8557 (mt-10) cc_final: 0.7412 (mt-10)
REVERT: A  106 ASP cc_start: 0.9183 (t70) cc_final: 0.8833 (t70)
REVERT: B   25 ASN cc_start: 0.7587 (t0) cc_final: 0.7151 (t0)
REVERT: B   26 ILE cc_start: 0.7781 (tp) cc_final: 0.7104 (tp)
REVERT: B   27 GLN cc_start: 0.8920 (mp10) cc_final: 0.8672 (mp10)
REVERT: B   29 ILE cc_start: 0.9656 (pt) cc_final: 0.9312 (mt)
REVERT: B   59 LYS cc_start: 0.9277 (tptm) cc_final: 0.9068 (tptm)
REVERT: B   74 GLU cc_start: 0.8297 (tm-30) cc_final: 0.8070 (tm-30)
REVERT: C   86 SER cc_start: 0.8032 (t) cc_final: 0.7732 (t)
REVERT: C   90 MET cc_start: 0.8779 (ptp) cc_final: 0.8561 (ptt)
REVERT: C   93 GLN cc_start: 0.8201 (pp30) cc_final: 0.7614 (pp30)
REVERT: C   97 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8616 (mt-10)
REVERT: D   44 LYS cc_start: 0.8921 (mmtt) cc_final: 0.8699 (mtpp)
REVERT: D   54 THR cc_start: 0.9231 (p) cc_final: 0.8838 (p)
REVERT: D   55 ARG cc_start: 0.8964 (mtt180) cc_final: 0.8240 (mmm-85)
REVERT: D   63 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8418 (tm-30)
REVERT: D   67 ARG cc_start: 0.9202 (mtp-110) cc_final: 0.8795 (mtm110)
REVERT: D   77 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7964 (mppt)
REVERT: E   68 GLN cc_start: 0.9181 (tp40) cc_final: 0.8775 (tp-100)
REVERT: E   76 GLN cc_start: 0.8960 (tt0) cc_final: 0.8447 (tp-100)
REVERT: E   93 GLN cc_start: 0.9298 (mm110) cc_final: 0.8946 (mm110)
REVERT: E  128 ARG cc_start: 0.8493 (mmm-85) cc_final: 0.7771 (mmm-85)
REVERT: F   29 ILE cc_start: 0.9545 (mm) cc_final: 0.9283 (mm)
REVERT: F   35 ARG cc_start: 0.9025 (mtp-110) cc_final: 0.8648 (ttm110)
REVERT: F   55 ARG cc_start: 0.8936 (mmt90) cc_final: 0.8642 (mmt90)
REVERT: F   63 GLU cc_start: 0.9398 (tt0) cc_final: 0.8795 (tm-30)
REVERT: F   64 ASN cc_start: 0.9226 (m-40) cc_final: 0.8408 (m-40)
REVERT: F   67 ARG cc_start: 0.9178 (ttp80) cc_final: 0.8251 (ttp-110)
REVERT: F   78 ARG cc_start: 0.8106 (ptm160) cc_final: 0.7813 (ptm160)
REVERT: F   82 THR cc_start: 0.8152 (p) cc_final: 0.7876 (p)
REVERT: F   88 TYR cc_start: 0.8771 (m-80) cc_final: 0.8480 (t80)
REVERT: G   73 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8701 (tm-30)
REVERT: G   80 THR cc_start: 0.8588 (p) cc_final: 0.8159 (p)
REVERT: G   97 GLU cc_start: 0.8029 (mp0) cc_final: 0.7793 (mt-10)
REVERT: G  106 ASP cc_start: 0.9152 (t0) cc_final: 0.8944 (t70)
REVERT: G  123 ASP cc_start: 0.8993 (m-30) cc_final: 0.8551 (m-30)
REVERT: G  128 ARG cc_start: 0.8931 (mtp-110) cc_final: 0.8146 (mtp-110)
REVERT: H   25 ASN cc_start: 0.8974 (p0) cc_final: 0.8679 (p0)
REVERT: H   43 VAL cc_start: 0.8079 (t) cc_final: 0.7677 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 276
  average time/residue: 0.1292
  time to fit residues: 46.2784
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  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 56 optimal weight:   20.0000
   chunk 10 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 48 optimal weight:    8.9990
   chunk 34 optimal weight:    3.9990
   chunk 77 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   overall best weight:    2.3988

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.061037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.047138 restraints weight = 59972.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.048362 restraints weight = 36774.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.049207 restraints weight = 26391.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.049778 restraints weight = 20918.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.050171 restraints weight = 17844.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          1.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073  10403  Z= 0.195
  Angle     :  0.688   8.181  15068  Z= 0.396
  Chirality :  0.036   0.165   1723
  Planarity :  0.005   0.064   1069
  Dihedral  : 32.710 178.061   3286
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 17.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.33), residues: 578
  helix:  0.86 (0.23), residues: 463
  sheet:  None (None), residues: 0
  loop : -1.81 (0.47), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  39 
 TYR   0.015   0.002   TYR F  51 
 PHE   0.022   0.002   PHE G 104 
 HIS   0.007   0.002   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (10403)
  covalent geometry    : angle       0.68820 (15068)
  hydrogen bonds       : bond        0.04321 (  663)
  hydrogen bonds       : angle       3.29933 ( 1649)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1560.20 seconds
wall clock time: 27 minutes 34.57 seconds (1654.57 seconds total)