Starting phenix.real_space_refine
on Tue Feb 11 07:21:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hf2_34710/02_2025/8hf2_34710.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hf2_34710/02_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_34710/02_2025/8hf2_34710.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hf2_34710/02_2025/8hf2_34710.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hf2_34710/02_2025/8hf2_34710.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hf2_34710/02_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 2.52, 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: 1.23
  Conformation dependent library (CDL) restraints added in 542.5 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: 0.38
  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: 1.31

  Time building geometry restraints manager: 1.43 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: 0.04
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:             0.630
  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:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     14.430
  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:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.190
-------------------------------------------------------------------------------
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= 0.762
  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 

*********************** 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  : 0.545 
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: 0.1797
  time to fit residues: 60.2194
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  : 0.501 
-------------------------------------------------------------------------------
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 = 31)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.065352 restraints weight = 11850.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.066842 restraints weight = 8678.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
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= 0.196
  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 

*********************** 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  : 0.472 
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: 0.9044 (pt) cc_final: 0.8814 (pt)
REVERT: B   94 HIS cc_start: 0.9351 (m90) cc_final: 0.8729 (m-70)
REVERT: B  107 LEU cc_start: 0.9495 (mt) cc_final: 0.9048 (mt)
REVERT: B  136 ASN cc_start: 0.9065 (p0) cc_final: 0.8659 (p0)
REVERT: C   44 GLN cc_start: 0.8793 (mt0) cc_final: 0.8278 (tt0)
REVERT: C   97 HIS cc_start: 0.9407 (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: 0.8858 (mt0) cc_final: 0.8376 (tt0)
REVERT: D   97 HIS cc_start: 0.9335 (m170) cc_final: 0.9104 (m170)
REVERT: D  136 ASN cc_start: 0.9061 (p0) cc_final: 0.8786 (p0)
REVERT: E   79 MET cc_start: 0.9465 (tmm) cc_final: 0.9147 (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: 0.1791
  time to fit residues: 48.9282
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  : 0.556 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 3 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 6 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    1.5990

-------------------------------------------------------------------------------
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 = 0.3381 r_free = 0.3381 target = 0.080681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.062863 restraints weight = 18866.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.064928 restraints weight = 11524.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.066310 restraints weight = 8229.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.5851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4770  Z= 0.197
  Angle     :  0.650  10.574   6500  Z= 0.316
  Chirality :  0.033   0.122    815
  Planarity :  0.004   0.027    770
  Dihedral  :  4.609  15.460    630
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  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:  0.09 (0.33), residues: 590
  helix:  0.84 (0.24), residues: 475
  sheet:  None (None), residues: 0
  loop : -3.14 (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   0.002   TYR D 132 
 ARG   0.003   0.000   ARG A  76 

*********************** 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
  230 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.9640 (m-80) cc_final: 0.9373 (m-80)
REVERT: A   76 ARG cc_start: 0.9318 (tpp80) cc_final: 0.9032 (mmm160)
REVERT: A   79 MET cc_start: 0.9351 (tmm) cc_final: 0.9126 (mtp)
REVERT: A   80 ASP cc_start: 0.8905 (t0) cc_final: 0.8393 (t0)
REVERT: A   94 HIS cc_start: 0.9190 (m90) cc_final: 0.8677 (m90)
REVERT: A  107 LEU cc_start: 0.9510 (mt) cc_final: 0.9183 (mt)
REVERT: B   53 LEU cc_start: 0.9008 (pt) cc_final: 0.8701 (pt)
REVERT: B   76 ARG cc_start: 0.9487 (tpp-160) cc_final: 0.9116 (mmm160)
REVERT: B   94 HIS cc_start: 0.9192 (m90) cc_final: 0.8797 (m90)
REVERT: B  107 LEU cc_start: 0.9481 (mt) cc_final: 0.9175 (mt)
REVERT: B  132 TYR cc_start: 0.8522 (t80) cc_final: 0.8288 (t80)
REVERT: B  136 ASN cc_start: 0.9071 (p0) cc_final: 0.8715 (p0)
REVERT: C   21 PHE cc_start: 0.8923 (t80) cc_final: 0.8686 (t80)
REVERT: C   76 ARG cc_start: 0.9346 (tpp80) cc_final: 0.8959 (mmm160)
REVERT: C   79 MET cc_start: 0.9442 (tmm) cc_final: 0.9216 (mtp)
REVERT: C   80 ASP cc_start: 0.8967 (t0) cc_final: 0.8355 (t0)
REVERT: C   91 LEU cc_start: 0.8682 (mp) cc_final: 0.8314 (tt)
REVERT: C   94 HIS cc_start: 0.9138 (m90) cc_final: 0.8627 (m90)
REVERT: C   97 HIS cc_start: 0.9452 (m170) cc_final: 0.9198 (m90)
REVERT: C  132 TYR cc_start: 0.8739 (t80) cc_final: 0.8433 (t80)
REVERT: D   53 LEU cc_start: 0.9169 (pt) cc_final: 0.8869 (pt)
REVERT: D   79 MET cc_start: 0.9507 (tmm) cc_final: 0.9300 (tmm)
REVERT: D   94 HIS cc_start: 0.9240 (m90) cc_final: 0.8762 (m90)
REVERT: D  107 LEU cc_start: 0.9279 (mp) cc_final: 0.9063 (mm)
REVERT: D  136 ASN cc_start: 0.9004 (p0) cc_final: 0.8795 (p0)
REVERT: E   21 PHE cc_start: 0.9042 (t80) cc_final: 0.8637 (t80)
REVERT: E   79 MET cc_start: 0.9265 (tmm) cc_final: 0.8944 (mtp)
REVERT: E   80 ASP cc_start: 0.8964 (t0) cc_final: 0.8314 (t0)
REVERT: E   94 HIS cc_start: 0.9130 (m90) cc_final: 0.8754 (m90)
REVERT: E   97 HIS cc_start: 0.9421 (m90) cc_final: 0.9072 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.1713
  time to fit residues: 48.9377
Evaluate side-chains
  190 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 52 optimal weight:    0.8980
   chunk 54 optimal weight:    9.9990
   chunk 3 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0870
   chunk 43 optimal weight:    9.9990
   chunk 50 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 42 optimal weight:    0.0470
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.5858

-------------------------------------------------------------------------------
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
B  97 HIS
D  97 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.083595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.065186 restraints weight = 18874.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.067320 restraints weight = 11760.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.068869 restraints weight = 8456.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.6554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4770  Z= 0.163
  Angle     :  0.610  10.566   6500  Z= 0.286
  Chirality :  0.033   0.126    815
  Planarity :  0.004   0.032    770
  Dihedral  :  4.378  13.818    630
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  5.10 %
    Favored  : 94.71 %
  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:  0.79 (0.34), residues: 590
  helix:  1.34 (0.24), residues: 475
  sheet:  None (None), residues: 0
  loop : -2.96 (0.41), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 126 
 HIS   0.012   0.002   HIS B  97 
 PHE   0.011   0.002   PHE C 115 
 TYR   0.020   0.002   TYR C  24 
 ARG   0.005   0.000   ARG E  76 

*********************** 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
  240 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 239
  time to evaluate  : 0.551 
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   53 LEU cc_start: 0.9018 (pt) cc_final: 0.8802 (pt)
REVERT: A   76 ARG cc_start: 0.9439 (tpp80) cc_final: 0.9122 (tpp80)
REVERT: A   94 HIS cc_start: 0.9047 (m90) cc_final: 0.8591 (m90)
REVERT: A   97 HIS cc_start: 0.9417 (m170) cc_final: 0.9168 (m90)
REVERT: B   94 HIS cc_start: 0.9083 (m90) cc_final: 0.8590 (m-70)
REVERT: B   97 HIS cc_start: 0.9322 (m170) cc_final: 0.8987 (m-70)
REVERT: B  132 TYR cc_start: 0.8544 (t80) cc_final: 0.8278 (t80)
REVERT: C   62 CYS cc_start: 0.8709 (m) cc_final: 0.8132 (p)
REVERT: C   76 ARG cc_start: 0.9400 (tpp80) cc_final: 0.9018 (tpp80)
REVERT: C   94 HIS cc_start: 0.9033 (m90) cc_final: 0.8705 (m-70)
REVERT: C   97 HIS cc_start: 0.9511 (m170) cc_final: 0.9303 (m-70)
REVERT: C  132 TYR cc_start: 0.8724 (t80) cc_final: 0.8409 (t80)
REVERT: D   21 PHE cc_start: 0.9067 (t80) cc_final: 0.8815 (t80)
REVERT: D   44 GLN cc_start: 0.8744 (mt0) cc_final: 0.8457 (tt0)
REVERT: D   53 LEU cc_start: 0.9134 (pt) cc_final: 0.8743 (pp)
REVERT: D   76 ARG cc_start: 0.9399 (tpp80) cc_final: 0.9173 (tpp80)
REVERT: D   91 LEU cc_start: 0.8599 (mp) cc_final: 0.8126 (tt)
REVERT: D   94 HIS cc_start: 0.8961 (m90) cc_final: 0.8517 (m90)
REVERT: D   97 HIS cc_start: 0.9369 (m170) cc_final: 0.9111 (m90)
REVERT: E   21 PHE cc_start: 0.9017 (t80) cc_final: 0.8685 (t80)
REVERT: E   76 ARG cc_start: 0.9252 (mmm160) cc_final: 0.8753 (mmm160)
REVERT: E   80 ASP cc_start: 0.8908 (t0) cc_final: 0.8568 (t0)
REVERT: E   91 LEU cc_start: 0.8621 (mp) cc_final: 0.8228 (tt)
REVERT: E   94 HIS cc_start: 0.9032 (m90) cc_final: 0.8713 (m90)
REVERT: E   97 HIS cc_start: 0.9421 (m170) cc_final: 0.9054 (m-70)
  outliers start: 1
  outliers final: 0
  residues processed: 239
  average time/residue: 0.1626
  time to fit residues: 48.6353
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  : 0.554 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 59 optimal weight:    9.9990
   chunk 52 optimal weight:    5.9990
   chunk 3 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 36 optimal weight:   10.0000
   chunk 22 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.3788

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.082188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.063482 restraints weight = 19161.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.065643 restraints weight = 11939.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.066967 restraints weight = 8624.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.6786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4770  Z= 0.181
  Angle     :  0.636  11.618   6500  Z= 0.307
  Chirality :  0.034   0.099    815
  Planarity :  0.004   0.032    770
  Dihedral  :  4.250  13.356    630
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  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:  0.89 (0.34), residues: 590
  helix:  1.39 (0.23), residues: 475
  sheet:  None (None), residues: 0
  loop : -2.88 (0.41), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 126 
 HIS   0.016   0.001   HIS D  29 
 PHE   0.023   0.002   PHE B  66 
 TYR   0.013   0.001   TYR B  70 
 ARG   0.002   0.000   ARG D  76 

*********************** 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
  219 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 0.501 
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   44 GLN cc_start: 0.9148 (tt0) cc_final: 0.8896 (tt0)
REVERT: A   66 PHE cc_start: 0.9594 (m-80) cc_final: 0.9208 (m-80)
REVERT: A   76 ARG cc_start: 0.9425 (tpp80) cc_final: 0.9101 (tpp80)
REVERT: A   94 HIS cc_start: 0.8973 (m90) cc_final: 0.8535 (m90)
REVERT: A   97 HIS cc_start: 0.9391 (m170) cc_final: 0.9065 (m90)
REVERT: B   94 HIS cc_start: 0.9107 (m90) cc_final: 0.8655 (m-70)
REVERT: B  132 TYR cc_start: 0.8540 (t80) cc_final: 0.8187 (t80)
REVERT: B  136 ASN cc_start: 0.8992 (p0) cc_final: 0.8553 (p0)
REVERT: C   44 GLN cc_start: 0.8378 (tm-30) cc_final: 0.7706 (tm-30)
REVERT: C   66 PHE cc_start: 0.9597 (m-80) cc_final: 0.9291 (m-80)
REVERT: C   76 ARG cc_start: 0.9418 (tpp80) cc_final: 0.8991 (tpp80)
REVERT: C   94 HIS cc_start: 0.9132 (m90) cc_final: 0.8789 (m90)
REVERT: C  132 TYR cc_start: 0.8748 (t80) cc_final: 0.8387 (t80)
REVERT: C  136 ASN cc_start: 0.9037 (p0) cc_final: 0.8617 (p0)
REVERT: D   44 GLN cc_start: 0.8578 (mt0) cc_final: 0.8372 (tt0)
REVERT: D   76 ARG cc_start: 0.9455 (tpp80) cc_final: 0.9093 (mmm160)
REVERT: D   79 MET cc_start: 0.9304 (tmm) cc_final: 0.8964 (mtp)
REVERT: D   80 ASP cc_start: 0.9160 (t0) cc_final: 0.8838 (t0)
REVERT: D   94 HIS cc_start: 0.8895 (m90) cc_final: 0.8481 (m90)
REVERT: D   97 HIS cc_start: 0.9322 (m170) cc_final: 0.8936 (m90)
REVERT: E   66 PHE cc_start: 0.9573 (m-80) cc_final: 0.9185 (m-80)
REVERT: E   76 ARG cc_start: 0.9299 (mmm160) cc_final: 0.8470 (mmm160)
REVERT: E   80 ASP cc_start: 0.9019 (t0) cc_final: 0.8779 (t0)
REVERT: E   94 HIS cc_start: 0.8927 (m90) cc_final: 0.8555 (m90)
REVERT: E   97 HIS cc_start: 0.9370 (m170) cc_final: 0.9078 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 219
  average time/residue: 0.1605
  time to fit residues: 44.4091
Evaluate side-chains
  188 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 10 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 23 optimal weight:    7.9990
   chunk 45 optimal weight:    6.9990
   chunk 24 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    3.3990

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.074161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.056440 restraints weight = 19603.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.058277 restraints weight = 12415.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.059536 restraints weight = 9011.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.6852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   4770  Z= 0.316
  Angle     :  0.725  12.234   6500  Z= 0.374
  Chirality :  0.035   0.151    815
  Planarity :  0.004   0.029    770
  Dihedral  :  4.497  13.560    630
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  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:  0.58 (0.33), residues: 590
  helix:  1.14 (0.23), residues: 475
  sheet:  None (None), residues: 0
  loop : -2.79 (0.40), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 123 
 HIS   0.026   0.003   HIS B  97 
 PHE   0.022   0.002   PHE D  66 
 TYR   0.019   0.003   TYR A  24 
 ARG   0.002   0.001   ARG D  76 

*********************** 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
  204 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.512 
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   44 GLN cc_start: 0.9217 (tt0) cc_final: 0.8675 (tm-30)
REVERT: A   76 ARG cc_start: 0.9438 (tpp80) cc_final: 0.9111 (tpp80)
REVERT: A   94 HIS cc_start: 0.9184 (m90) cc_final: 0.8698 (m90)
REVERT: A  136 ASN cc_start: 0.9110 (p0) cc_final: 0.8848 (p0)
REVERT: B   76 ARG cc_start: 0.9475 (tpp80) cc_final: 0.9124 (tpp80)
REVERT: B   94 HIS cc_start: 0.9052 (m90) cc_final: 0.8398 (m-70)
REVERT: B  132 TYR cc_start: 0.8531 (t80) cc_final: 0.8234 (t80)
REVERT: B  136 ASN cc_start: 0.9050 (p0) cc_final: 0.8713 (p0)
REVERT: C   76 ARG cc_start: 0.9435 (tpp80) cc_final: 0.9025 (tpp80)
REVERT: C   94 HIS cc_start: 0.9150 (m90) cc_final: 0.8797 (m90)
REVERT: C   97 HIS cc_start: 0.9334 (m170) cc_final: 0.9129 (m90)
REVERT: C  132 TYR cc_start: 0.8786 (t80) cc_final: 0.8462 (t80)
REVERT: D   76 ARG cc_start: 0.9463 (tpp80) cc_final: 0.9127 (tpp80)
REVERT: D   91 LEU cc_start: 0.8811 (mp) cc_final: 0.8555 (pp)
REVERT: D   94 HIS cc_start: 0.9100 (m90) cc_final: 0.8345 (m-70)
REVERT: E   44 GLN cc_start: 0.9224 (tt0) cc_final: 0.8599 (tm-30)
REVERT: E   76 ARG cc_start: 0.9313 (mmm160) cc_final: 0.9028 (tpp80)
REVERT: E   80 ASP cc_start: 0.9291 (t0) cc_final: 0.9012 (t0)
REVERT: E   94 HIS cc_start: 0.9073 (m90) cc_final: 0.8561 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.1595
  time to fit residues: 41.1320
Evaluate side-chains
  168 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 39 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 136 ASN
** D  97 HIS ** 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 = 0.3397 r_free = 0.3397 target = 0.079665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.061484 restraints weight = 18696.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.063577 restraints weight = 11618.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.065146 restraints weight = 8354.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.7252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   4770  Z= 0.197
  Angle     :  0.664  11.368   6500  Z= 0.320
  Chirality :  0.033   0.111    815
  Planarity :  0.004   0.034    770
  Dihedral  :  4.373  15.448    630
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  2.55 %
    Favored  : 97.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.34), residues: 590
  helix:  1.30 (0.23), residues: 475
  sheet:  None (None), residues: 0
  loop : -2.67 (0.42), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 123 
 HIS   0.028   0.004   HIS A  97 
 PHE   0.017   0.002   PHE D  66 
 TYR   0.023   0.002   TYR A  24 
 ARG   0.003   0.000   ARG D  74 

*********************** 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
  217 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 216
  time to evaluate  : 0.546 
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   44 GLN cc_start: 0.9197 (tt0) cc_final: 0.8513 (tm-30)
REVERT: A   76 ARG cc_start: 0.9437 (tpp80) cc_final: 0.9099 (tpp80)
REVERT: A   94 HIS cc_start: 0.8766 (m90) cc_final: 0.8297 (m90)
REVERT: B   53 LEU cc_start: 0.8905 (pt) cc_final: 0.8692 (pt)
REVERT: B   76 ARG cc_start: 0.9484 (tpp80) cc_final: 0.9227 (tpp80)
REVERT: B   94 HIS cc_start: 0.8713 (m90) cc_final: 0.8309 (m-70)
REVERT: B  132 TYR cc_start: 0.8519 (t80) cc_final: 0.8246 (t80)
REVERT: B  136 ASN cc_start: 0.9020 (p0) cc_final: 0.8646 (p0)
REVERT: C   66 PHE cc_start: 0.9622 (m-80) cc_final: 0.9175 (m-80)
REVERT: C   76 ARG cc_start: 0.9421 (tpp80) cc_final: 0.9017 (tpp80)
REVERT: C   94 HIS cc_start: 0.9055 (m90) cc_final: 0.8736 (m90)
REVERT: C  132 TYR cc_start: 0.8778 (t80) cc_final: 0.8446 (t80)
REVERT: C  136 ASN cc_start: 0.9080 (p0) cc_final: 0.8856 (p0)
REVERT: D   44 GLN cc_start: 0.8893 (tt0) cc_final: 0.8511 (tm-30)
REVERT: D   76 ARG cc_start: 0.9453 (tpp80) cc_final: 0.8990 (mmm160)
REVERT: D   79 MET cc_start: 0.9313 (tmm) cc_final: 0.8948 (mtp)
REVERT: D   80 ASP cc_start: 0.9176 (t0) cc_final: 0.8812 (t0)
REVERT: D   94 HIS cc_start: 0.8693 (m90) cc_final: 0.8321 (m90)
REVERT: E   42 LEU cc_start: 0.8833 (mm) cc_final: 0.8631 (mm)
REVERT: E   76 ARG cc_start: 0.9281 (mmm160) cc_final: 0.8415 (mmm160)
REVERT: E   80 ASP cc_start: 0.9215 (t0) cc_final: 0.8789 (t0)
REVERT: E   94 HIS cc_start: 0.8865 (m90) cc_final: 0.8499 (m90)
  outliers start: 1
  outliers final: 1
  residues processed: 216
  average time/residue: 0.1567
  time to fit residues: 42.8566
Evaluate side-chains
  182 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 181
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 57 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.9786

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.080561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.062002 restraints weight = 18971.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.064123 restraints weight = 12049.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.065676 restraints weight = 8788.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.7580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   4770  Z= 0.202
  Angle     :  0.685  12.313   6500  Z= 0.331
  Chirality :  0.033   0.102    815
  Planarity :  0.004   0.039    770
  Dihedral  :  4.290  13.803    630
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.33), residues: 590
  helix:  1.30 (0.23), residues: 475
  sheet:  None (None), residues: 0
  loop : -2.49 (0.44), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 126 
 HIS   0.023   0.003   HIS D  97 
 PHE   0.017   0.002   PHE E  66 
 TYR   0.020   0.002   TYR B  24 
 ARG   0.002   0.000   ARG B  76 

*********************** 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
  212 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLN cc_start: 0.9111 (tt0) cc_final: 0.8813 (tt0)
REVERT: A   76 ARG cc_start: 0.9425 (tpp80) cc_final: 0.9002 (mmm160)
REVERT: A   79 MET cc_start: 0.9291 (tmm) cc_final: 0.8866 (mtp)
REVERT: A   80 ASP cc_start: 0.9091 (t0) cc_final: 0.8748 (t0)
REVERT: A   94 HIS cc_start: 0.8720 (m90) cc_final: 0.8290 (m90)
REVERT: B   76 ARG cc_start: 0.9431 (tpp80) cc_final: 0.9074 (mmm160)
REVERT: B   79 MET cc_start: 0.9300 (tmm) cc_final: 0.8995 (mtp)
REVERT: B   80 ASP cc_start: 0.9116 (t0) cc_final: 0.8839 (t0)
REVERT: B   94 HIS cc_start: 0.8635 (m90) cc_final: 0.8287 (m-70)
REVERT: B  132 TYR cc_start: 0.8383 (t80) cc_final: 0.8111 (t80)
REVERT: B  136 ASN cc_start: 0.8986 (p0) cc_final: 0.8602 (p0)
REVERT: C   44 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8558 (pp30)
REVERT: C   66 PHE cc_start: 0.9607 (m-80) cc_final: 0.9045 (m-80)
REVERT: C   76 ARG cc_start: 0.9416 (tpp80) cc_final: 0.9050 (tpp80)
REVERT: C   77 GLU cc_start: 0.9418 (mm-30) cc_final: 0.9029 (mm-30)
REVERT: C   94 HIS cc_start: 0.8898 (m90) cc_final: 0.8670 (m90)
REVERT: C  102 LEU cc_start: 0.9475 (tp) cc_final: 0.9106 (mt)
REVERT: C  132 TYR cc_start: 0.8789 (t80) cc_final: 0.8463 (t80)
REVERT: C  136 ASN cc_start: 0.9122 (p0) cc_final: 0.8841 (p0)
REVERT: D   66 PHE cc_start: 0.9596 (m-80) cc_final: 0.9156 (m-80)
REVERT: D   76 ARG cc_start: 0.9389 (tpp80) cc_final: 0.8954 (mmm160)
REVERT: D   79 MET cc_start: 0.9376 (tmm) cc_final: 0.9061 (mtp)
REVERT: D   80 ASP cc_start: 0.9202 (t0) cc_final: 0.8731 (t0)
REVERT: D   94 HIS cc_start: 0.8655 (m90) cc_final: 0.8263 (m90)
REVERT: E   53 LEU cc_start: 0.8999 (pt) cc_final: 0.8753 (mt)
REVERT: E   76 ARG cc_start: 0.9260 (mmm160) cc_final: 0.8385 (mmm160)
REVERT: E   80 ASP cc_start: 0.9198 (t0) cc_final: 0.8655 (t0)
REVERT: E   94 HIS cc_start: 0.8735 (m90) cc_final: 0.8364 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.1499
  time to fit residues: 40.3868
Evaluate side-chains
  186 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 43 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 14 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.7582

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.081026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.062253 restraints weight = 18418.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.064445 restraints weight = 11837.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.065907 restraints weight = 8627.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.7753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4770  Z= 0.198
  Angle     :  0.691  12.464   6500  Z= 0.328
  Chirality :  0.034   0.121    815
  Planarity :  0.004   0.042    770
  Dihedral  :  4.233  14.268    630
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 10.32
  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:  0.95 (0.33), residues: 590
  helix:  1.34 (0.23), residues: 475
  sheet:  None (None), residues: 0
  loop : -2.36 (0.44), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E 123 
 HIS   0.013   0.002   HIS C  97 
 PHE   0.020   0.002   PHE B  63 
 TYR   0.019   0.002   TYR B  24 
 ARG   0.001   0.000   ARG E  90 

*********************** 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
  217 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.491 
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   44 GLN cc_start: 0.9106 (tt0) cc_final: 0.8896 (tt0)
REVERT: A   76 ARG cc_start: 0.9424 (tpp80) cc_final: 0.8998 (mmm160)
REVERT: A   79 MET cc_start: 0.9271 (tmm) cc_final: 0.8900 (mtp)
REVERT: A   80 ASP cc_start: 0.9078 (t0) cc_final: 0.8646 (t0)
REVERT: A   94 HIS cc_start: 0.8710 (m90) cc_final: 0.8310 (m90)
REVERT: B   53 LEU cc_start: 0.8978 (pt) cc_final: 0.8774 (pt)
REVERT: B   62 CYS cc_start: 0.9092 (m) cc_final: 0.8823 (m)
REVERT: B   76 ARG cc_start: 0.9396 (tpp80) cc_final: 0.9148 (tpp80)
REVERT: B   94 HIS cc_start: 0.8413 (m90) cc_final: 0.8144 (m-70)
REVERT: B  132 TYR cc_start: 0.8439 (t80) cc_final: 0.8190 (t80)
REVERT: B  136 ASN cc_start: 0.9034 (p0) cc_final: 0.8636 (p0)
REVERT: C   44 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8334 (pp30)
REVERT: C   62 CYS cc_start: 0.8912 (m) cc_final: 0.8558 (m)
REVERT: C   66 PHE cc_start: 0.9598 (m-80) cc_final: 0.9260 (m-80)
REVERT: C   76 ARG cc_start: 0.9385 (tpp80) cc_final: 0.8698 (mmm160)
REVERT: C   77 GLU cc_start: 0.9403 (mm-30) cc_final: 0.9079 (mm-30)
REVERT: C   79 MET cc_start: 0.9246 (tmm) cc_final: 0.9019 (tmm)
REVERT: C   94 HIS cc_start: 0.8842 (m90) cc_final: 0.8597 (m90)
REVERT: C  132 TYR cc_start: 0.8759 (t80) cc_final: 0.8433 (t80)
REVERT: C  136 ASN cc_start: 0.9083 (p0) cc_final: 0.8858 (p0)
REVERT: D   66 PHE cc_start: 0.9549 (m-80) cc_final: 0.9166 (m-80)
REVERT: D   76 ARG cc_start: 0.9354 (tpp80) cc_final: 0.9009 (mmm160)
REVERT: D   79 MET cc_start: 0.9358 (tmm) cc_final: 0.8982 (mtp)
REVERT: D   94 HIS cc_start: 0.8686 (m90) cc_final: 0.8326 (m90)
REVERT: E   53 LEU cc_start: 0.9042 (pt) cc_final: 0.8752 (mt)
REVERT: E   66 PHE cc_start: 0.9548 (m-80) cc_final: 0.9104 (m-80)
REVERT: E   76 ARG cc_start: 0.9242 (mmm160) cc_final: 0.8388 (mmm160)
REVERT: E   80 ASP cc_start: 0.9198 (t0) cc_final: 0.8618 (t0)
REVERT: E   94 HIS cc_start: 0.8697 (m90) cc_final: 0.8410 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.1499
  time to fit residues: 41.4878
Evaluate side-chains
  192 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 21 optimal weight:    0.6980
   chunk 11 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 59 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9980
   chunk 14 optimal weight:    6.9990
   chunk 55 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    2.2984

-------------------------------------------------------------------------------
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 = 0.3342 r_free = 0.3342 target = 0.076401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.058771 restraints weight = 19341.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.060676 restraints weight = 12207.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.062075 restraints weight = 8852.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.7670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4770  Z= 0.260
  Angle     :  0.724  13.572   6500  Z= 0.358
  Chirality :  0.035   0.124    815
  Planarity :  0.005   0.043    770
  Dihedral  :  4.381  13.852    630
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.33), residues: 590
  helix:  1.31 (0.23), residues: 475
  sheet:  None (None), residues: 0
  loop : -2.33 (0.43), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 126 
 HIS   0.012   0.002   HIS C  97 
 PHE   0.027   0.002   PHE B  63 
 TYR   0.017   0.002   TYR D  70 
 ARG   0.003   0.001   ARG E  74 

********************** 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
  208 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLN cc_start: 0.9056 (tt0) cc_final: 0.8845 (tt0)
REVERT: A   76 ARG cc_start: 0.9428 (tpp80) cc_final: 0.8958 (mmm160)
REVERT: A   79 MET cc_start: 0.9235 (tmm) cc_final: 0.8997 (mtp)
REVERT: A   80 ASP cc_start: 0.9213 (t0) cc_final: 0.8790 (t0)
REVERT: A   94 HIS cc_start: 0.8796 (m90) cc_final: 0.8291 (m90)
REVERT: B   29 HIS cc_start: 0.9524 (m170) cc_final: 0.9196 (m170)
REVERT: B   62 CYS cc_start: 0.9069 (m) cc_final: 0.8808 (m)
REVERT: B   76 ARG cc_start: 0.9401 (tpp80) cc_final: 0.9165 (tpp80)
REVERT: B   94 HIS cc_start: 0.8570 (m90) cc_final: 0.8014 (m-70)
REVERT: B  132 TYR cc_start: 0.8448 (t80) cc_final: 0.8132 (t80)
REVERT: B  136 ASN cc_start: 0.9041 (p0) cc_final: 0.8694 (p0)
REVERT: C   44 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8576 (tm-30)
REVERT: C   76 ARG cc_start: 0.9380 (tpp80) cc_final: 0.9019 (tpp80)
REVERT: C   77 GLU cc_start: 0.9379 (mm-30) cc_final: 0.9066 (mm-30)
REVERT: C   94 HIS cc_start: 0.9064 (m90) cc_final: 0.8671 (m90)
REVERT: C  132 TYR cc_start: 0.8830 (t80) cc_final: 0.8445 (t80)
REVERT: D   44 GLN cc_start: 0.9009 (tt0) cc_final: 0.8774 (tm-30)
REVERT: D   76 ARG cc_start: 0.9345 (tpp80) cc_final: 0.8920 (mmm160)
REVERT: D   80 ASP cc_start: 0.9183 (t0) cc_final: 0.8803 (t0)
REVERT: D   94 HIS cc_start: 0.8916 (m90) cc_final: 0.8417 (m90)
REVERT: E   39 ILE cc_start: 0.9533 (tp) cc_final: 0.9258 (tt)
REVERT: E   76 ARG cc_start: 0.9353 (mmm160) cc_final: 0.8488 (mmm160)
REVERT: E   80 ASP cc_start: 0.9359 (t0) cc_final: 0.8774 (t0)
REVERT: E   94 HIS cc_start: 0.8751 (m90) cc_final: 0.8404 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 208
  average time/residue: 0.1514
  time to fit residues: 40.4301
Evaluate side-chains
  183 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 52 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 10 optimal weight:    0.1980
   chunk 56 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 3 optimal weight:    8.9990
   chunk 53 optimal weight:    0.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    1.2386

-------------------------------------------------------------------------------
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 = 0.3379 r_free = 0.3379 target = 0.078393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.060014 restraints weight = 18614.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.062032 restraints weight = 11901.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.063268 restraints weight = 8654.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.7886

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= 0.209
  Angle     :  0.691  12.788   6500  Z= 0.328
  Chirality :  0.035   0.123    815
  Planarity :  0.004   0.045    770
  Dihedral  :  4.331  14.850    630
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  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:  0.94 (0.34), residues: 590
  helix:  1.32 (0.23), residues: 475
  sheet:  None (None), residues: 0
  loop : -2.29 (0.44), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E 123 
 HIS   0.013   0.002   HIS C  97 
 PHE   0.023   0.002   PHE B  63 
 TYR   0.010   0.001   TYR D  70 
 ARG   0.002   0.000   ARG E  76 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1704.55 seconds
wall clock time: 31 minutes 12.80 seconds (1872.80 seconds total)