Starting phenix.real_space_refine
on Thu Jun  5 00:32:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hf2_34710/06_2025/8hf2_34710.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hf2_34710/06_2025/8hf2_34710.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hf2_34710/06_2025/8hf2_34710.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hf2_34710/06_2025/8hf2_34710.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hf2_34710/06_2025/8hf2_34710.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hf2_34710/06_2025/8hf2_34710.cif"
  }
  resolution = 4.14
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.014
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: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    3125      2.51       5
     N     760      2.21       5
     O     755      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 4660
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 932
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 932
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 2.51, per 1000 atoms: 0.54
  Number of scatterers: 4660
  At special positions: 0
  Unit cell: (87.98, 85.86, 67.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O     755      8.00
     N     760      7.00
     C    3125      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: 1.14
  Conformation dependent library (CDL) restraints added in 637.6 milliseconds
  

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1130

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 0 sheets defined
      84.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 43
      removed outlier: 4.149A  pdb=" N   THR A  23 " --> pdb=" O   VAL A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 46
      No H-bonds generated for 'chain 'A' and resid 44 through 46'
    Processing helix  chain 'A' and resid 56 through 80
      removed outlier: 3.933A  pdb=" N   PHE A  60 " --> pdb=" O   HIS A  56 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   VAL A  65 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ARG A  76 " --> pdb=" O   VAL A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 110
      removed outlier: 3.574A  pdb=" N   ILE A  92 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLY A 100 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLY A 101 " --> pdb=" O   HIS A  97 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   VAL A 110 " --> pdb=" O   VAL A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 136
    Processing helix  chain 'B' and resid 20 through 43
    Processing helix  chain 'B' and resid 44 through 46
      No H-bonds generated for 'chain 'B' and resid 44 through 46'
    Processing helix  chain 'B' and resid 56 through 80
      removed outlier: 3.933A  pdb=" N   PHE B  60 " --> pdb=" O   HIS B  56 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   VAL B  65 " --> pdb=" O   LEU B  61 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ARG B  76 " --> pdb=" O   VAL B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 110
      removed outlier: 3.573A  pdb=" N   ILE B  92 " --> pdb=" O   VAL B  88 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   GLY B 100 " --> pdb=" O   SER B  96 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLY B 101 " --> pdb=" O   HIS B  97 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   VAL B 110 " --> pdb=" O   VAL B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 136
    Processing helix  chain 'C' and resid 20 through 43
    Processing helix  chain 'C' and resid 44 through 46
      No H-bonds generated for 'chain 'C' and resid 44 through 46'
    Processing helix  chain 'C' and resid 56 through 80
      removed outlier: 3.933A  pdb=" N   PHE C  60 " --> pdb=" O   HIS C  56 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   VAL C  65 " --> pdb=" O   LEU C  61 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ARG C  76 " --> pdb=" O   VAL C  72 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 110
      removed outlier: 3.574A  pdb=" N   ILE C  92 " --> pdb=" O   VAL C  88 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLY C 100 " --> pdb=" O   SER C  96 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLY C 101 " --> pdb=" O   HIS C  97 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   VAL C 110 " --> pdb=" O   VAL C 106 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 136
    Processing helix  chain 'D' and resid 20 through 43
    Processing helix  chain 'D' and resid 44 through 46
      No H-bonds generated for 'chain 'D' and resid 44 through 46'
    Processing helix  chain 'D' and resid 56 through 80
      removed outlier: 3.932A  pdb=" N   PHE D  60 " --> pdb=" O   HIS D  56 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   VAL D  65 " --> pdb=" O   LEU D  61 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ARG D  76 " --> pdb=" O   VAL D  72 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 86 through 110
      removed outlier: 3.575A  pdb=" N   ILE D  92 " --> pdb=" O   VAL D  88 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLY D 100 " --> pdb=" O   SER D  96 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLY D 101 " --> pdb=" O   HIS D  97 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   VAL D 110 " --> pdb=" O   VAL D 106 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 113 through 136
    Processing helix  chain 'E' and resid 20 through 43
    Processing helix  chain 'E' and resid 44 through 46
      No H-bonds generated for 'chain 'E' and resid 44 through 46'
    Processing helix  chain 'E' and resid 56 through 80
      removed outlier: 3.934A  pdb=" N   PHE E  60 " --> pdb=" O   HIS E  56 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   VAL E  65 " --> pdb=" O   LEU E  61 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ARG E  76 " --> pdb=" O   VAL E  72 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 110
      removed outlier: 3.574A  pdb=" N   ILE E  92 " --> pdb=" O   VAL E  88 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLY E 100 " --> pdb=" O   SER E  96 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLY E 101 " --> pdb=" O   HIS E  97 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   VAL E 110 " --> pdb=" O   VAL E 106 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 113 through 136

    375 hydrogen bonds defined for protein.
    1125 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.25

  Time building geometry restraints manager: 1.36 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1393
        1.34 -     1.46: 1172
        1.46 -     1.58: 2175
        1.58 -     1.69: 0
        1.69 -     1.81: 30
  Bond restraints: 4770
  Sorted by residual:
  bond pdb=" CG  LEU A  40 "
       pdb=" CD1 LEU A  40 "
    ideal  model  delta    sigma   weight residual
    1.521  1.451  0.070 3.30e-02 9.18e+02 4.44e+00
  bond pdb=" CG  LEU E  40 "
       pdb=" CD1 LEU E  40 "
    ideal  model  delta    sigma   weight residual
    1.521  1.452  0.069 3.30e-02 9.18e+02 4.37e+00
  bond pdb=" CG  LEU B  40 "
       pdb=" CD1 LEU B  40 "
    ideal  model  delta    sigma   weight residual
    1.521  1.452  0.069 3.30e-02 9.18e+02 4.36e+00
  bond pdb=" CG  LEU D  40 "
       pdb=" CD1 LEU D  40 "
    ideal  model  delta    sigma   weight residual
    1.521  1.453  0.068 3.30e-02 9.18e+02 4.30e+00
  bond pdb=" CG  LEU C  40 "
       pdb=" CD1 LEU C  40 "
    ideal  model  delta    sigma   weight residual
    1.521  1.453  0.068 3.30e-02 9.18e+02 4.29e+00
  ... (remaining 4765 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 6140
        1.96 -     3.92: 297
        3.92 -     5.88: 43
        5.88 -     7.84: 10
        7.84 -     9.80: 10
  Bond angle restraints: 6500
  Sorted by residual:
  angle pdb=" CA  LEU E  42 "
        pdb=" CB  LEU E  42 "
        pdb=" CG  LEU E  42 "
      ideal   model   delta    sigma   weight residual
     116.30  106.50    9.80 3.50e+00 8.16e-02 7.84e+00
  angle pdb=" CA  LEU D  42 "
        pdb=" CB  LEU D  42 "
        pdb=" CG  LEU D  42 "
      ideal   model   delta    sigma   weight residual
     116.30  106.53    9.77 3.50e+00 8.16e-02 7.80e+00
  angle pdb=" CA  LEU C  42 "
        pdb=" CB  LEU C  42 "
        pdb=" CG  LEU C  42 "
      ideal   model   delta    sigma   weight residual
     116.30  106.55    9.75 3.50e+00 8.16e-02 7.76e+00
  angle pdb=" CA  LEU A  42 "
        pdb=" CB  LEU A  42 "
        pdb=" CG  LEU A  42 "
      ideal   model   delta    sigma   weight residual
     116.30  106.56    9.74 3.50e+00 8.16e-02 7.74e+00
  angle pdb=" CA  LEU B  42 "
        pdb=" CB  LEU B  42 "
        pdb=" CG  LEU B  42 "
      ideal   model   delta    sigma   weight residual
     116.30  106.56    9.74 3.50e+00 8.16e-02 7.74e+00
  ... (remaining 6495 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.57: 2192
       10.57 -    21.14: 336
       21.14 -    31.71: 107
       31.71 -    42.28: 90
       42.28 -    52.85: 20
  Dihedral angle restraints: 2745
    sinusoidal: 1005
      harmonic: 1740
  Sorted by residual:
  dihedral pdb=" CA  LEU C  43 "
           pdb=" C   LEU C  43 "
           pdb=" N   GLN C  44 "
           pdb=" CA  GLN C  44 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.03   23.97     0      5.00e+00 4.00e-02 2.30e+01
  dihedral pdb=" CA  LEU A  43 "
           pdb=" C   LEU A  43 "
           pdb=" N   GLN A  44 "
           pdb=" CA  GLN A  44 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.04   23.96     0      5.00e+00 4.00e-02 2.30e+01
  dihedral pdb=" CA  LEU E  43 "
           pdb=" C   LEU E  43 "
           pdb=" N   GLN E  44 "
           pdb=" CA  GLN E  44 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.04   23.96     0      5.00e+00 4.00e-02 2.30e+01
  ... (remaining 2742 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 436
       0.031 -    0.063: 244
       0.063 -    0.094: 97
       0.094 -    0.126: 23
       0.126 -    0.157: 15
  Chirality restraints: 815
  Sorted by residual:
  chirality pdb=" CB  VAL E  28 "
            pdb=" CA  VAL E  28 "
            pdb=" CG1 VAL E  28 "
            pdb=" CG2 VAL E  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.16e-01
  chirality pdb=" CA  LEU C  43 "
            pdb=" N   LEU C  43 "
            pdb=" C   LEU C  43 "
            pdb=" CB  LEU C  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.92e-01
  chirality pdb=" CB  VAL B  28 "
            pdb=" CA  VAL B  28 "
            pdb=" CG1 VAL B  28 "
            pdb=" CG2 VAL B  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.90e-01
  ... (remaining 812 not shown)

  Planarity restraints: 770
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E  24 "    0.014 2.00e-02 2.50e+03   7.98e-03 1.27e+00
        pdb=" CG  TYR E  24 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 TYR E  24 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR E  24 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR E  24 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR E  24 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR E  24 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR E  24 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C  36 "   -0.006 2.00e-02 2.50e+03   1.13e-02 1.27e+00
        pdb=" CG  ASN C  36 "    0.019 2.00e-02 2.50e+03
        pdb=" OD1 ASN C  36 "   -0.007 2.00e-02 2.50e+03
        pdb=" ND2 ASN C  36 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  24 "    0.014 2.00e-02 2.50e+03   7.94e-03 1.26e+00
        pdb=" CG  TYR D  24 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  24 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  24 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  24 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  24 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  24 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR D  24 "    0.005 2.00e-02 2.50e+03
  ... (remaining 767 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1362
        2.79 -     3.32: 5357
        3.32 -     3.85: 7557
        3.85 -     4.37: 8194
        4.37 -     4.90: 13136
  Nonbonded interactions: 35606
  Sorted by model distance:
  nonbonded pdb=" O   LYS C  20 "
            pdb=" OG1 THR C  23 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   LYS A  20 "
            pdb=" OG1 THR A  23 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   LYS D  20 "
            pdb=" OG1 THR D  23 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   LYS E  20 "
            pdb=" OG1 THR E  23 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   LYS B  20 "
            pdb=" OG1 THR B  23 "
     model   vdw
     2.265 3.040
  ... (remaining 35601 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

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:             0.960
  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:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.330
  Find NCS groups from input model:        0.090
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
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      :  0.012   0.070   4770  Z= 0.524
  Angle     :  1.036   9.803   6500  Z= 0.550
  Chirality :  0.047   0.157    815
  Planarity :  0.004   0.025    770
  Dihedral  : 14.202  52.847   1615
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 15.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.39 (0.26), residues: 590
  helix: -2.42 (0.18), residues: 470
  sheet:  None (None), residues: 0
  loop : -4.02 (0.48), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 126 
 HIS   0.002   0.001   HIS E  56 
 PHE   0.011   0.002   PHE E 120 
 TYR   0.017   0.004   TYR E  24 
 ARG   0.003   0.001   ARG E  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10564 (  375)
  hydrogen bonds       : angle       5.87529 ( 1125)
  covalent geometry    : bond        0.01211 ( 4770)
  covalent geometry    : angle       1.03638 ( 6500)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 272
  time to evaluate  : 0.484 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  136 ASN cc_start: 0.8097 (p0) cc_final: 0.7781 (p0)
REVERT: C   44 GLN cc_start: 0.8039 (mt0) cc_final: 0.7525 (tt0)
REVERT: C  132 TYR cc_start: 0.8429 (t80) cc_final: 0.8192 (t80)
REVERT: D   43 LEU cc_start: 0.9300 (pp) cc_final: 0.9035 (tt)
REVERT: D   44 GLN cc_start: 0.8146 (mt0) cc_final: 0.7552 (tt0)
REVERT: D  136 ASN cc_start: 0.8198 (p0) cc_final: 0.7674 (p0)
REVERT: E   63 PHE cc_start: 0.8584 (t80) cc_final: 0.8311 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 272
  average time/residue: 0.1689
  time to fit residues: 56.4858
Evaluate side-chains
  166 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0070
   chunk 30 optimal weight:   20.0000
   chunk 24 optimal weight:    3.9990
   chunk 47 optimal weight:   10.0000
   chunk 18 optimal weight:    8.9990
   chunk 28 optimal weight:    1.9990
   chunk 35 optimal weight:    8.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    1.1602

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

Flipped N/Q/H residues before XYZ refinement:
E  97 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.082016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.063327 restraints weight = 18564.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.065339 restraints weight = 11848.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.066821 restraints weight = 8724.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.4809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4770  Z= 0.141
  Angle     :  0.693  10.318   6500  Z= 0.334
  Chirality :  0.036   0.144    815
  Planarity :  0.004   0.042    770
  Dihedral  :  5.200  16.756    630
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.32), residues: 590
  helix:  0.05 (0.23), residues: 475
  sheet:  None (None), residues: 0
  loop : -3.41 (0.36), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 126 
 HIS   0.007   0.002   HIS E  29 
 PHE   0.014   0.001   PHE D  63 
 TYR   0.009   0.002   TYR E 132 
 ARG   0.003   0.001   ARG E  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04745 (  375)
  hydrogen bonds       : angle       3.99284 ( 1125)
  covalent geometry    : bond        0.00301 ( 4770)
  covalent geometry    : angle       0.69336 ( 6500)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.534 
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   76 ARG cc_start: 0.9197 (tpp80) cc_final: 0.8970 (tpp80)
REVERT: A   97 HIS cc_start: 0.9428 (m170) cc_final: 0.9073 (m90)
REVERT: A  107 LEU cc_start: 0.9541 (mt) cc_final: 0.9241 (mt)
REVERT: B   53 LEU cc_start: 0.9045 (pt) cc_final: 0.8814 (pt)
REVERT: B   94 HIS cc_start: 0.9351 (m90) cc_final: 0.8728 (m-70)
REVERT: B  107 LEU cc_start: 0.9495 (mt) cc_final: 0.9049 (mt)
REVERT: B  136 ASN cc_start: 0.9066 (p0) cc_final: 0.8659 (p0)
REVERT: C   44 GLN cc_start: 0.8793 (mt0) cc_final: 0.8277 (tt0)
REVERT: C   97 HIS cc_start: 0.9408 (m170) cc_final: 0.9159 (m90)
REVERT: C  132 TYR cc_start: 0.8783 (t80) cc_final: 0.8431 (t80)
REVERT: D   44 GLN cc_start: 0.8857 (mt0) cc_final: 0.8374 (tt0)
REVERT: D   97 HIS cc_start: 0.9334 (m170) cc_final: 0.9103 (m170)
REVERT: D  136 ASN cc_start: 0.9060 (p0) cc_final: 0.8786 (p0)
REVERT: E   79 MET cc_start: 0.9465 (tmm) cc_final: 0.9146 (tmm)
REVERT: E   97 HIS cc_start: 0.9362 (m-70) cc_final: 0.9108 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 224
  average time/residue: 0.1802
  time to fit residues: 49.2156
Evaluate side-chains
  178 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 15 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 6 optimal weight:   10.0000
   chunk 8 optimal weight:    0.8980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
** B  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  29 HIS
E  97 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.081937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.063904 restraints weight = 18812.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.066011 restraints weight = 11554.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.067453 restraints weight = 8261.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.5903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4770  Z= 0.132
  Angle     :  0.646  10.428   6500  Z= 0.311
  Chirality :  0.033   0.114    815
  Planarity :  0.004   0.026    770
  Dihedral  :  4.567  15.374    630
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.34), residues: 590
  helix:  0.94 (0.24), residues: 475
  sheet:  None (None), residues: 0
  loop : -3.15 (0.38), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 123 
 HIS   0.020   0.003   HIS E  97 
 PHE   0.016   0.001   PHE A  63 
 TYR   0.008   0.001   TYR E 132 
 ARG   0.003   0.000   ARG A  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03887 (  375)
  hydrogen bonds       : angle       3.74783 ( 1125)
  covalent geometry    : bond        0.00284 ( 4770)
  covalent geometry    : angle       0.64634 ( 6500)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 0.525 
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: symmetry clash
   revert: symmetry clash
REVERT: A   42 LEU cc_start: 0.9057 (mm) cc_final: 0.8772 (mm)
REVERT: A   66 PHE cc_start: 0.9625 (m-80) cc_final: 0.9369 (m-80)
REVERT: A   76 ARG cc_start: 0.9312 (tpp80) cc_final: 0.9028 (mmm160)
REVERT: A   79 MET cc_start: 0.9341 (tmm) cc_final: 0.9116 (mtp)
REVERT: A   80 ASP cc_start: 0.8937 (t0) cc_final: 0.8413 (t0)
REVERT: A   94 HIS cc_start: 0.9192 (m90) cc_final: 0.8674 (m90)
REVERT: A  107 LEU cc_start: 0.9487 (mt) cc_final: 0.9158 (mt)
REVERT: B   53 LEU cc_start: 0.9002 (pt) cc_final: 0.8698 (pt)
REVERT: B   76 ARG cc_start: 0.9494 (tpp-160) cc_final: 0.9125 (mmm160)
REVERT: B   94 HIS cc_start: 0.9169 (m90) cc_final: 0.8718 (m90)
REVERT: B  107 LEU cc_start: 0.9459 (mt) cc_final: 0.9159 (mt)
REVERT: B  132 TYR cc_start: 0.8516 (t80) cc_final: 0.8269 (t80)
REVERT: B  136 ASN cc_start: 0.9071 (p0) cc_final: 0.8712 (p0)
REVERT: C   21 PHE cc_start: 0.8898 (t80) cc_final: 0.8657 (t80)
REVERT: C   76 ARG cc_start: 0.9321 (tpp80) cc_final: 0.8971 (mmm160)
REVERT: C   80 ASP cc_start: 0.8944 (t0) cc_final: 0.8302 (t0)
REVERT: C   91 LEU cc_start: 0.8677 (mp) cc_final: 0.8321 (tt)
REVERT: C   94 HIS cc_start: 0.9098 (m90) cc_final: 0.8615 (m90)
REVERT: C   97 HIS cc_start: 0.9461 (m170) cc_final: 0.9202 (m90)
REVERT: C  132 TYR cc_start: 0.8735 (t80) cc_final: 0.8432 (t80)
REVERT: D   53 LEU cc_start: 0.9206 (pt) cc_final: 0.8944 (pp)
REVERT: D   94 HIS cc_start: 0.9199 (m90) cc_final: 0.8724 (m90)
REVERT: D  107 LEU cc_start: 0.9215 (mp) cc_final: 0.9012 (mm)
REVERT: D  136 ASN cc_start: 0.8978 (p0) cc_final: 0.8774 (p0)
REVERT: E   21 PHE cc_start: 0.9024 (t80) cc_final: 0.8609 (t80)
REVERT: E   79 MET cc_start: 0.9230 (tmm) cc_final: 0.8881 (mtp)
REVERT: E   80 ASP cc_start: 0.8942 (t0) cc_final: 0.8265 (t0)
REVERT: E   91 LEU cc_start: 0.8687 (mp) cc_final: 0.8368 (tt)
REVERT: E   94 HIS cc_start: 0.9128 (m90) cc_final: 0.8779 (m90)
REVERT: E   97 HIS cc_start: 0.9402 (m90) cc_final: 0.9013 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 234
  average time/residue: 0.1653
  time to fit residues: 48.0107
Evaluate side-chains
  189 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 20 optimal weight:    8.9990
   chunk 52 optimal weight:    0.7980
   chunk 54 optimal weight:    6.9990
   chunk 3 optimal weight:    0.0870
   chunk 22 optimal weight:    0.9980
   chunk 6 optimal weight:    8.9990
   chunk 43 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 45 optimal weight:   10.0000
   chunk 42 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.5762

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
B  44 GLN
D  97 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.078851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.061207 restraints weight = 18995.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.063179 restraints weight = 11727.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.064595 restraints weight = 8397.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.6425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4770  Z= 0.134
  Angle     :  0.622  11.449   6500  Z= 0.303
  Chirality :  0.034   0.123    815
  Planarity :  0.004   0.033    770
  Dihedral  :  4.403  14.223    630
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  5.49 %
    Favored  : 94.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.34), residues: 590
  helix:  1.25 (0.24), residues: 475
  sheet:  None (None), residues: 0
  loop : -2.96 (0.40), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 126 
 HIS   0.019   0.002   HIS B  97 
 PHE   0.022   0.002   PHE B  66 
 TYR   0.020   0.002   TYR C  24 
 ARG   0.004   0.000   ARG C  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03617 (  375)
  hydrogen bonds       : angle       3.76749 ( 1125)
  covalent geometry    : bond        0.00298 ( 4770)
  covalent geometry    : angle       0.62207 ( 6500)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 221
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 ARG cc_start: 0.9399 (tpp80) cc_final: 0.9109 (tpp80)
REVERT: A   94 HIS cc_start: 0.9111 (m90) cc_final: 0.8635 (m90)
REVERT: B   94 HIS cc_start: 0.9218 (m90) cc_final: 0.8570 (m-70)
REVERT: B  132 TYR cc_start: 0.8560 (t80) cc_final: 0.8285 (t80)
REVERT: C   62 CYS cc_start: 0.8785 (m) cc_final: 0.8256 (p)
REVERT: C   76 ARG cc_start: 0.9372 (tpp80) cc_final: 0.8820 (mmm160)
REVERT: C   94 HIS cc_start: 0.9146 (m90) cc_final: 0.8777 (m90)
REVERT: C   97 HIS cc_start: 0.9543 (m170) cc_final: 0.9281 (m-70)
REVERT: C  132 TYR cc_start: 0.8772 (t80) cc_final: 0.8441 (t80)
REVERT: D   44 GLN cc_start: 0.8746 (mt0) cc_final: 0.8444 (tt0)
REVERT: D   76 ARG cc_start: 0.9406 (tpp80) cc_final: 0.8968 (tpp80)
REVERT: D   91 LEU cc_start: 0.8721 (mp) cc_final: 0.8230 (tt)
REVERT: D   94 HIS cc_start: 0.9035 (m90) cc_final: 0.8549 (m90)
REVERT: D   97 HIS cc_start: 0.9347 (m170) cc_final: 0.9121 (m90)
REVERT: D  107 LEU cc_start: 0.9321 (mp) cc_final: 0.9120 (mm)
REVERT: E   21 PHE cc_start: 0.9094 (t80) cc_final: 0.8827 (t80)
REVERT: E   76 ARG cc_start: 0.9273 (mmm160) cc_final: 0.8458 (mmm160)
REVERT: E   80 ASP cc_start: 0.9039 (t0) cc_final: 0.8835 (t0)
REVERT: E   94 HIS cc_start: 0.8986 (m90) cc_final: 0.8624 (m90)
REVERT: E   97 HIS cc_start: 0.9483 (m170) cc_final: 0.9088 (m-70)
  outliers start: 1
  outliers final: 0
  residues processed: 221
  average time/residue: 0.1598
  time to fit residues: 44.5558
Evaluate side-chains
  181 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 49 optimal weight:    0.0980
   chunk 17 optimal weight:    0.9990
   chunk 59 optimal weight:    8.9990
   chunk 52 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 36 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 44 optimal weight:    8.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.2186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.081537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.063000 restraints weight = 19158.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.065056 restraints weight = 12079.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.066554 restraints weight = 8736.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.6815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4770  Z= 0.126
  Angle     :  0.627  10.385   6500  Z= 0.306
  Chirality :  0.034   0.104    815
  Planarity :  0.004   0.032    770
  Dihedral  :  4.317  13.643    630
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.34), residues: 590
  helix:  1.35 (0.24), residues: 475
  sheet:  None (None), residues: 0
  loop : -2.83 (0.41), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 123 
 HIS   0.016   0.002   HIS A  97 
 PHE   0.023   0.002   PHE A  66 
 TYR   0.022   0.002   TYR A  24 
 ARG   0.002   0.000   ARG A  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03483 (  375)
  hydrogen bonds       : angle       3.70430 ( 1125)
  covalent geometry    : bond        0.00285 ( 4770)
  covalent geometry    : angle       0.62745 ( 6500)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 0.488 
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   66 PHE cc_start: 0.9605 (m-80) cc_final: 0.9197 (m-80)
REVERT: A   76 ARG cc_start: 0.9462 (tpp80) cc_final: 0.9133 (tpp80)
REVERT: A   94 HIS cc_start: 0.8955 (m90) cc_final: 0.8457 (m90)
REVERT: B   77 GLU cc_start: 0.8950 (tp30) cc_final: 0.8625 (mm-30)
REVERT: B   94 HIS cc_start: 0.9065 (m90) cc_final: 0.8481 (m-70)
REVERT: B  132 TYR cc_start: 0.8500 (t80) cc_final: 0.8185 (t80)
REVERT: B  136 ASN cc_start: 0.9014 (p0) cc_final: 0.8613 (p0)
REVERT: C   66 PHE cc_start: 0.9513 (m-80) cc_final: 0.9252 (m-80)
REVERT: C   76 ARG cc_start: 0.9401 (tpp80) cc_final: 0.8838 (mmm160)
REVERT: C   94 HIS cc_start: 0.9036 (m90) cc_final: 0.8612 (m-70)
REVERT: C  102 LEU cc_start: 0.9382 (mt) cc_final: 0.9126 (tp)
REVERT: C  132 TYR cc_start: 0.8757 (t80) cc_final: 0.8407 (t80)
REVERT: C  136 ASN cc_start: 0.9044 (p0) cc_final: 0.8631 (p0)
REVERT: D   76 ARG cc_start: 0.9474 (tpp80) cc_final: 0.9030 (tpp80)
REVERT: D   94 HIS cc_start: 0.8935 (m90) cc_final: 0.8507 (m90)
REVERT: D   97 HIS cc_start: 0.9410 (m170) cc_final: 0.9064 (m90)
REVERT: E   76 ARG cc_start: 0.9279 (mmm160) cc_final: 0.8740 (mmm160)
REVERT: E   80 ASP cc_start: 0.9112 (t0) cc_final: 0.8829 (t0)
REVERT: E   91 LEU cc_start: 0.8672 (mp) cc_final: 0.8292 (tt)
REVERT: E   94 HIS cc_start: 0.8867 (m90) cc_final: 0.8366 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 222
  average time/residue: 0.1502
  time to fit residues: 42.0976
Evaluate side-chains
  189 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 47 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 23 optimal weight:    6.9990
   chunk 45 optimal weight:    0.7980
   chunk 24 optimal weight:   10.0000
   chunk 26 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
C  97 HIS
** E  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  97 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.080471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.062230 restraints weight = 19070.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.064310 restraints weight = 11821.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 17)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.065568 restraints weight = 8481.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.7088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4770  Z= 0.126
  Angle     :  0.652  11.943   6500  Z= 0.314
  Chirality :  0.033   0.091    815
  Planarity :  0.004   0.033    770
  Dihedral  :  4.320  13.619    630
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.33), residues: 590
  helix:  1.39 (0.23), residues: 475
  sheet:  None (None), residues: 0
  loop : -2.73 (0.42), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.002   TRP C 123 
 HIS   0.014   0.002   HIS C  97 
 PHE   0.017   0.002   PHE A  66 
 TYR   0.019   0.002   TYR D  24 
 ARG   0.003   0.000   ARG A  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03418 (  375)
  hydrogen bonds       : angle       3.77698 ( 1125)
  covalent geometry    : bond        0.00279 ( 4770)
  covalent geometry    : angle       0.65166 ( 6500)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.531 
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   76 ARG cc_start: 0.9444 (tpp80) cc_final: 0.9120 (tpp80)
REVERT: A   94 HIS cc_start: 0.8857 (m90) cc_final: 0.8304 (m90)
REVERT: B   76 ARG cc_start: 0.9438 (tpp80) cc_final: 0.9178 (tpp80)
REVERT: B   77 GLU cc_start: 0.8983 (tp30) cc_final: 0.8757 (tp30)
REVERT: B   94 HIS cc_start: 0.8977 (m90) cc_final: 0.8358 (m-70)
REVERT: B  132 TYR cc_start: 0.8502 (t80) cc_final: 0.8234 (t80)
REVERT: B  136 ASN cc_start: 0.9015 (p0) cc_final: 0.8605 (p0)
REVERT: C   62 CYS cc_start: 0.8806 (m) cc_final: 0.8475 (m)
REVERT: C   66 PHE cc_start: 0.9487 (m-80) cc_final: 0.9053 (m-80)
REVERT: C   76 ARG cc_start: 0.9392 (tpp80) cc_final: 0.8816 (mmm160)
REVERT: C   94 HIS cc_start: 0.9053 (m90) cc_final: 0.8590 (m-70)
REVERT: C  132 TYR cc_start: 0.8776 (t80) cc_final: 0.8450 (t80)
REVERT: C  136 ASN cc_start: 0.9056 (p0) cc_final: 0.8849 (p0)
REVERT: D   44 GLN cc_start: 0.9015 (tt0) cc_final: 0.8587 (tm-30)
REVERT: D   76 ARG cc_start: 0.9454 (tpp80) cc_final: 0.9045 (tpp80)
REVERT: D   94 HIS cc_start: 0.8860 (m90) cc_final: 0.8362 (m90)
REVERT: E   44 GLN cc_start: 0.9080 (tt0) cc_final: 0.8809 (tt0)
REVERT: E   76 ARG cc_start: 0.9285 (mmm160) cc_final: 0.8463 (mmm160)
REVERT: E   77 GLU cc_start: 0.8913 (tp30) cc_final: 0.8711 (mm-30)
REVERT: E   80 ASP cc_start: 0.9162 (t0) cc_final: 0.8823 (t0)
REVERT: E   91 LEU cc_start: 0.8746 (mp) cc_final: 0.8319 (tt)
REVERT: E   94 HIS cc_start: 0.8946 (m90) cc_final: 0.8422 (m-70)
REVERT: E   97 HIS cc_start: 0.9306 (m170) cc_final: 0.9065 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.1535
  time to fit residues: 42.8621
Evaluate side-chains
  187 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 56 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** C  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  97 HIS
E  44 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.080483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.062411 restraints weight = 18642.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.064429 restraints weight = 11569.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.065928 restraints weight = 8370.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.7332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   4770  Z= 0.128
  Angle     :  0.645  10.772   6500  Z= 0.314
  Chirality :  0.033   0.114    815
  Planarity :  0.004   0.033    770
  Dihedral  :  4.243  12.811    630
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.34), residues: 590
  helix:  1.39 (0.23), residues: 475
  sheet:  None (None), residues: 0
  loop : -2.64 (0.43), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.064   0.002   TRP C 123 
 HIS   0.028   0.003   HIS C  97 
 PHE   0.020   0.002   PHE B  63 
 TYR   0.023   0.002   TYR D  24 
 ARG   0.002   0.000   ARG A  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03441 (  375)
  hydrogen bonds       : angle       3.71580 ( 1125)
  covalent geometry    : bond        0.00305 ( 4770)
  covalent geometry    : angle       0.64471 ( 6500)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.624 
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   76 ARG cc_start: 0.9438 (tpp80) cc_final: 0.8858 (mmm160)
REVERT: A   94 HIS cc_start: 0.8759 (m90) cc_final: 0.8295 (m90)
REVERT: B   62 CYS cc_start: 0.9015 (m) cc_final: 0.8784 (m)
REVERT: B   76 ARG cc_start: 0.9366 (tpp80) cc_final: 0.9068 (tpp80)
REVERT: B   94 HIS cc_start: 0.8928 (m90) cc_final: 0.8336 (m-70)
REVERT: B  132 TYR cc_start: 0.8508 (t80) cc_final: 0.8235 (t80)
REVERT: B  136 ASN cc_start: 0.9025 (p0) cc_final: 0.8647 (p0)
REVERT: C   62 CYS cc_start: 0.8792 (m) cc_final: 0.8441 (m)
REVERT: C   66 PHE cc_start: 0.9452 (m-80) cc_final: 0.9072 (m-80)
REVERT: C   76 ARG cc_start: 0.9367 (tpp80) cc_final: 0.8427 (mmm160)
REVERT: C   94 HIS cc_start: 0.8836 (m90) cc_final: 0.8460 (m-70)
REVERT: C  123 TRP cc_start: 0.9378 (t60) cc_final: 0.9145 (t-100)
REVERT: C  132 TYR cc_start: 0.8752 (t80) cc_final: 0.8405 (t80)
REVERT: C  136 ASN cc_start: 0.9061 (p0) cc_final: 0.8839 (p0)
REVERT: D   44 GLN cc_start: 0.8952 (tt0) cc_final: 0.8578 (tm-30)
REVERT: D   53 LEU cc_start: 0.8850 (pt) cc_final: 0.8594 (pt)
REVERT: D   66 PHE cc_start: 0.9578 (m-80) cc_final: 0.9237 (m-80)
REVERT: D   76 ARG cc_start: 0.9416 (tpp80) cc_final: 0.8696 (mmm160)
REVERT: D   80 ASP cc_start: 0.9144 (t0) cc_final: 0.8831 (t0)
REVERT: D   94 HIS cc_start: 0.8770 (m90) cc_final: 0.8411 (m-70)
REVERT: E   76 ARG cc_start: 0.9273 (mmm160) cc_final: 0.8889 (mmm160)
REVERT: E   77 GLU cc_start: 0.9046 (tp30) cc_final: 0.8815 (mm-30)
REVERT: E   94 HIS cc_start: 0.8794 (m90) cc_final: 0.8353 (m-70)
REVERT: E  136 ASN cc_start: 0.9126 (p0) cc_final: 0.8844 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 213
  average time/residue: 0.1540
  time to fit residues: 41.8358
Evaluate side-chains
  189 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 59 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 47 optimal weight:    8.9990
   chunk 28 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
C  97 HIS
** E  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  44 GLN
E 136 ASN

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 = 0.079720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.062112 restraints weight = 18970.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.064244 restraints weight = 11700.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.065651 restraints weight = 8315.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.7557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4770  Z= 0.129
  Angle     :  0.666  12.501   6500  Z= 0.324
  Chirality :  0.034   0.134    815
  Planarity :  0.004   0.036    770
  Dihedral  :  4.276  15.476    630
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.57 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.33), residues: 590
  helix:  1.28 (0.23), residues: 475
  sheet:  None (None), residues: 0
  loop : -2.51 (0.43), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP C 123 
 HIS   0.024   0.003   HIS C  97 
 PHE   0.018   0.002   PHE B  63 
 TYR   0.020   0.002   TYR B  24 
 ARG   0.002   0.000   ARG A  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03513 (  375)
  hydrogen bonds       : angle       3.84236 ( 1125)
  covalent geometry    : bond        0.00294 ( 4770)
  covalent geometry    : angle       0.66635 ( 6500)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 215
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.9621 (m-80) cc_final: 0.9209 (m-80)
REVERT: A   76 ARG cc_start: 0.9369 (tpp80) cc_final: 0.8741 (mmm160)
REVERT: A   94 HIS cc_start: 0.8746 (m90) cc_final: 0.8276 (m90)
REVERT: B   53 LEU cc_start: 0.8893 (pt) cc_final: 0.8468 (pt)
REVERT: B   62 CYS cc_start: 0.9121 (m) cc_final: 0.8892 (m)
REVERT: B   76 ARG cc_start: 0.9403 (tpp80) cc_final: 0.9015 (mmm160)
REVERT: B   79 MET cc_start: 0.9347 (tmm) cc_final: 0.9119 (mtp)
REVERT: B   80 ASP cc_start: 0.8957 (t0) cc_final: 0.8600 (t0)
REVERT: B   94 HIS cc_start: 0.8814 (m90) cc_final: 0.8262 (m-70)
REVERT: B  132 TYR cc_start: 0.8416 (t80) cc_final: 0.8126 (t80)
REVERT: B  136 ASN cc_start: 0.9002 (p0) cc_final: 0.8639 (p0)
REVERT: C   62 CYS cc_start: 0.8769 (m) cc_final: 0.8417 (m)
REVERT: C   66 PHE cc_start: 0.9453 (m-80) cc_final: 0.9025 (m-80)
REVERT: C   76 ARG cc_start: 0.9328 (tpp80) cc_final: 0.8880 (mmm160)
REVERT: C   79 MET cc_start: 0.9279 (tmm) cc_final: 0.9023 (mtp)
REVERT: C   80 ASP cc_start: 0.9137 (t0) cc_final: 0.8620 (t0)
REVERT: C   94 HIS cc_start: 0.8870 (m90) cc_final: 0.8550 (m-70)
REVERT: C   97 HIS cc_start: 0.9421 (m90) cc_final: 0.8934 (m-70)
REVERT: C  132 TYR cc_start: 0.8780 (t80) cc_final: 0.8404 (t80)
REVERT: C  136 ASN cc_start: 0.9000 (p0) cc_final: 0.8787 (p0)
REVERT: D   44 GLN cc_start: 0.8969 (tt0) cc_final: 0.8675 (tm-30)
REVERT: D   53 LEU cc_start: 0.8828 (pt) cc_final: 0.8610 (pt)
REVERT: D   66 PHE cc_start: 0.9589 (m-80) cc_final: 0.9163 (m-80)
REVERT: D   76 ARG cc_start: 0.9405 (tpp80) cc_final: 0.8750 (mmm160)
REVERT: D   80 ASP cc_start: 0.9164 (t0) cc_final: 0.8808 (t0)
REVERT: D   94 HIS cc_start: 0.8776 (m90) cc_final: 0.8397 (m-70)
REVERT: E   76 ARG cc_start: 0.9294 (mmm160) cc_final: 0.8393 (mmm160)
REVERT: E   80 ASP cc_start: 0.9124 (t0) cc_final: 0.8818 (t0)
REVERT: E   94 HIS cc_start: 0.8720 (m90) cc_final: 0.8296 (m90)
  outliers start: 1
  outliers final: 0
  residues processed: 215
  average time/residue: 0.1449
  time to fit residues: 39.5610
Evaluate side-chains
  187 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 39 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 43 optimal weight:    8.9990
   chunk 46 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   overall best weight:    1.3384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.078723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.061097 restraints weight = 18810.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.063121 restraints weight = 11530.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.064575 restraints weight = 8220.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.7605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4770  Z= 0.137
  Angle     :  0.686  13.024   6500  Z= 0.331
  Chirality :  0.034   0.125    815
  Planarity :  0.004   0.039    770
  Dihedral  :  4.240  12.517    630
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.33), residues: 590
  helix:  1.29 (0.23), residues: 475
  sheet:  None (None), residues: 0
  loop : -2.42 (0.43), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 123 
 HIS   0.015   0.003   HIS E  97 
 PHE   0.018   0.002   PHE E  66 
 TYR   0.020   0.002   TYR B  24 
 ARG   0.001   0.000   ARG D  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03529 (  375)
  hydrogen bonds       : angle       3.86537 ( 1125)
  covalent geometry    : bond        0.00316 ( 4770)
  covalent geometry    : angle       0.68635 ( 6500)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.9610 (m-80) cc_final: 0.9193 (m-80)
REVERT: A   76 ARG cc_start: 0.9429 (tpp80) cc_final: 0.8768 (mmm160)
REVERT: A   94 HIS cc_start: 0.8741 (m90) cc_final: 0.8253 (m90)
REVERT: B   62 CYS cc_start: 0.9064 (m) cc_final: 0.8770 (m)
REVERT: B   76 ARG cc_start: 0.9379 (tpp80) cc_final: 0.9046 (mmm160)
REVERT: B   79 MET cc_start: 0.9259 (tmm) cc_final: 0.9033 (mtp)
REVERT: B   80 ASP cc_start: 0.9096 (t0) cc_final: 0.8699 (t0)
REVERT: B   94 HIS cc_start: 0.8774 (m90) cc_final: 0.8220 (m-70)
REVERT: B  132 TYR cc_start: 0.8521 (t80) cc_final: 0.8250 (t80)
REVERT: B  136 ASN cc_start: 0.9048 (p0) cc_final: 0.8671 (p0)
REVERT: C   76 ARG cc_start: 0.9349 (tpp80) cc_final: 0.8899 (mmm160)
REVERT: C   79 MET cc_start: 0.9227 (tmm) cc_final: 0.9010 (mtp)
REVERT: C   80 ASP cc_start: 0.9143 (t0) cc_final: 0.8642 (t0)
REVERT: C   94 HIS cc_start: 0.9028 (m90) cc_final: 0.8607 (m-70)
REVERT: C  132 TYR cc_start: 0.8790 (t80) cc_final: 0.8382 (t80)
REVERT: D   44 GLN cc_start: 0.9037 (tt0) cc_final: 0.8432 (tm-30)
REVERT: D   46 VAL cc_start: 0.9386 (p) cc_final: 0.9112 (t)
REVERT: D   66 PHE cc_start: 0.9573 (m-80) cc_final: 0.9168 (m-80)
REVERT: D   76 ARG cc_start: 0.9382 (tpp80) cc_final: 0.8754 (mmm160)
REVERT: D   80 ASP cc_start: 0.9180 (t0) cc_final: 0.8773 (t0)
REVERT: D   94 HIS cc_start: 0.8770 (m90) cc_final: 0.8365 (m-70)
REVERT: E   39 ILE cc_start: 0.9455 (tp) cc_final: 0.9171 (tt)
REVERT: E   66 PHE cc_start: 0.9495 (m-80) cc_final: 0.9260 (m-80)
REVERT: E   76 ARG cc_start: 0.9248 (mmm160) cc_final: 0.8400 (mmm160)
REVERT: E   80 ASP cc_start: 0.9161 (t0) cc_final: 0.8757 (t0)
REVERT: E   94 HIS cc_start: 0.8717 (m90) cc_final: 0.8379 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 209
  average time/residue: 0.1443
  time to fit residues: 38.3099
Evaluate side-chains
  187 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 47 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 59 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
E  44 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.080599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.062503 restraints weight = 19021.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.064591 restraints weight = 11904.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.066153 restraints weight = 8596.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.7925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4770  Z= 0.130
  Angle     :  0.686  12.675   6500  Z= 0.331
  Chirality :  0.035   0.143    815
  Planarity :  0.004   0.043    770
  Dihedral  :  4.234  12.478    630
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.33), residues: 590
  helix:  1.35 (0.23), residues: 475
  sheet:  None (None), residues: 0
  loop : -2.30 (0.44), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP C 123 
 HIS   0.012   0.002   HIS C  97 
 PHE   0.050   0.002   PHE C  66 
 TYR   0.020   0.002   TYR B  24 
 ARG   0.002   0.000   ARG E  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03471 (  375)
  hydrogen bonds       : angle       3.84544 ( 1125)
  covalent geometry    : bond        0.00301 ( 4770)
  covalent geometry    : angle       0.68638 ( 6500)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 CYS cc_start: 0.8910 (m) cc_final: 0.8553 (m)
REVERT: A   66 PHE cc_start: 0.9611 (m-80) cc_final: 0.9254 (m-80)
REVERT: A   76 ARG cc_start: 0.9445 (tpp80) cc_final: 0.9028 (mmm160)
REVERT: A   79 MET cc_start: 0.9264 (tmm) cc_final: 0.8866 (mtp)
REVERT: A   80 ASP cc_start: 0.9073 (t0) cc_final: 0.8771 (t0)
REVERT: A   94 HIS cc_start: 0.8744 (m90) cc_final: 0.8333 (m90)
REVERT: B   62 CYS cc_start: 0.9023 (m) cc_final: 0.8769 (m)
REVERT: B   76 ARG cc_start: 0.9379 (tpp80) cc_final: 0.9033 (mmm160)
REVERT: B   79 MET cc_start: 0.9233 (tmm) cc_final: 0.9005 (mtp)
REVERT: B   80 ASP cc_start: 0.9069 (t0) cc_final: 0.8614 (t0)
REVERT: B   94 HIS cc_start: 0.8655 (m90) cc_final: 0.8178 (m-70)
REVERT: B  132 TYR cc_start: 0.8405 (t80) cc_final: 0.8131 (t80)
REVERT: B  136 ASN cc_start: 0.8993 (p0) cc_final: 0.8605 (p0)
REVERT: C   76 ARG cc_start: 0.9404 (tpp80) cc_final: 0.8999 (mmm160)
REVERT: C   79 MET cc_start: 0.9234 (tmm) cc_final: 0.8953 (mtp)
REVERT: C   80 ASP cc_start: 0.9233 (t0) cc_final: 0.8777 (t0)
REVERT: C   94 HIS cc_start: 0.8877 (m90) cc_final: 0.8522 (m-70)
REVERT: C  132 TYR cc_start: 0.8764 (t80) cc_final: 0.8368 (t80)
REVERT: C  136 ASN cc_start: 0.9034 (p0) cc_final: 0.8751 (p0)
REVERT: D   44 GLN cc_start: 0.8977 (tt0) cc_final: 0.8635 (tm-30)
REVERT: D   66 PHE cc_start: 0.9584 (m-80) cc_final: 0.9183 (m-80)
REVERT: D   76 ARG cc_start: 0.9364 (tpp80) cc_final: 0.8726 (mmm160)
REVERT: D   79 MET cc_start: 0.9359 (tmm) cc_final: 0.9121 (tmm)
REVERT: D   80 ASP cc_start: 0.9203 (t0) cc_final: 0.8696 (t0)
REVERT: D   94 HIS cc_start: 0.8704 (m90) cc_final: 0.8387 (m-70)
REVERT: E   39 ILE cc_start: 0.9431 (tp) cc_final: 0.9143 (tt)
REVERT: E   66 PHE cc_start: 0.9476 (m-80) cc_final: 0.9129 (m-80)
REVERT: E   76 ARG cc_start: 0.9319 (mmm160) cc_final: 0.8485 (mmm160)
REVERT: E   80 ASP cc_start: 0.9183 (t0) cc_final: 0.8758 (t0)
REVERT: E   94 HIS cc_start: 0.8464 (m90) cc_final: 0.8115 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 209
  average time/residue: 0.1457
  time to fit residues: 38.8586
Evaluate side-chains
  189 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 56 optimal weight:    6.9990
   chunk 13 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0000
   overall best weight:    0.6986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.081966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.064140 restraints weight = 18817.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.066232 restraints weight = 11698.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.067646 restraints weight = 8358.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.8086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4770  Z= 0.128
  Angle     :  0.685  13.195   6500  Z= 0.327
  Chirality :  0.035   0.163    815
  Planarity :  0.004   0.042    770
  Dihedral  :  4.171  12.630    630
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.33), residues: 590
  helix:  1.34 (0.23), residues: 475
  sheet:  None (None), residues: 0
  loop : -2.36 (0.43), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP C 123 
 HIS   0.012   0.002   HIS E  97 
 PHE   0.035   0.002   PHE C  66 
 TYR   0.015   0.002   TYR B  70 
 ARG   0.001   0.000   ARG E  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03343 (  375)
  hydrogen bonds       : angle       3.82174 ( 1125)
  covalent geometry    : bond        0.00294 ( 4770)
  covalent geometry    : angle       0.68489 ( 6500)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1812.35 seconds
wall clock time: 32 minutes 11.77 seconds (1931.77 seconds total)