Starting phenix.real_space_refine
on Fri Aug 22 15:04:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hf2_34710/08_2025/8hf2_34710.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hf2_34710/08_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_34710/08_2025/8hf2_34710.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hf2_34710/08_2025/8hf2_34710.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hf2_34710/08_2025/8hf2_34710.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hf2_34710/08_2025/8hf2_34710.cif"
  }
  resolution = 4.14
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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:
    B, C, D, E
  Time building chain proxies: 0.85, per 1000 atoms: 0.18
  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: 0.49
  Conformation dependent library (CDL) restraints added in 206.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.09
  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: 0.70

  Time building geometry restraints manager: 0.61 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             1.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.900
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.640
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.003   0.001   ARG E  76 
 TYR   0.017   0.004   TYR E  24 
 PHE   0.011   0.002   PHE E 120 
 TRP   0.012   0.002   TRP C 126 
 HIS   0.002   0.001   HIS E  56 

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

*********************** 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  : 0.201 
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: 0.9036 (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: 0.8310 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 272
  average time/residue: 0.0620
  time to fit residues: 21.0124
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  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0000
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.7788

-------------------------------------------------------------------------------
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 = 0.3431 r_free = 0.3431 target = 0.083190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.064289 restraints weight = 18927.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.066385 restraints weight = 11969.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.067949 restraints weight = 8709.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.069057 restraints weight = 6904.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.069872 restraints weight = 5775.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.4846

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= 0.140
  Angle     :  0.706  10.338   6500  Z= 0.335
  Chirality :  0.036   0.160    815
  Planarity :  0.005   0.045    770
  Dihedral  :  5.168  16.669    630
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.86 (0.32), residues: 590
  helix:  0.16 (0.23), residues: 475
  sheet:  None (None), residues: 0
  loop : -3.45 (0.36), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  74 
 TYR   0.009   0.002   TYR E 132 
 PHE   0.015   0.001   PHE D  63 
 TRP   0.014   0.002   TRP B 126 
 HIS   0.006   0.002   HIS E  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 4770)
  covalent geometry    : angle       0.70556 ( 6500)
  hydrogen bonds       : bond        0.04654 (  375)
  hydrogen bonds       : angle       3.91377 ( 1125)

*********************** 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
  225 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.110 
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: symmetry clash
REVERT: A   39 ILE cc_start: 0.9383 (tt) cc_final: 0.9160 (tt)
REVERT: A   42 LEU cc_start: 0.9077 (mm) cc_final: 0.8757 (mm)
REVERT: A   76 ARG cc_start: 0.9188 (tpp80) cc_final: 0.8965 (tpp80)
REVERT: A   97 HIS cc_start: 0.9417 (m170) cc_final: 0.9071 (m90)
REVERT: A  107 LEU cc_start: 0.9519 (mt) cc_final: 0.9209 (mt)
REVERT: B   53 LEU cc_start: 0.8977 (pt) cc_final: 0.8757 (pt)
REVERT: B   94 HIS cc_start: 0.9386 (m90) cc_final: 0.8698 (m-70)
REVERT: B  107 LEU cc_start: 0.9499 (mt) cc_final: 0.9078 (mt)
REVERT: B  136 ASN cc_start: 0.9020 (p0) cc_final: 0.8606 (p0)
REVERT: C   97 HIS cc_start: 0.9387 (m170) cc_final: 0.9142 (m90)
REVERT: C  132 TYR cc_start: 0.8793 (t80) cc_final: 0.8430 (t80)
REVERT: D   24 TYR cc_start: 0.8810 (t80) cc_final: 0.8580 (t80)
REVERT: D   44 GLN cc_start: 0.8881 (mt0) cc_final: 0.8557 (tt0)
REVERT: D   97 HIS cc_start: 0.9322 (m170) cc_final: 0.8976 (m170)
REVERT: D  136 ASN cc_start: 0.9021 (p0) cc_final: 0.8748 (p0)
REVERT: E   32 LEU cc_start: 0.9278 (tt) cc_final: 0.9059 (tt)
REVERT: E   44 GLN cc_start: 0.8921 (mt0) cc_final: 0.8615 (tp40)
REVERT: E   97 HIS cc_start: 0.9468 (m170) cc_final: 0.9162 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 225
  average time/residue: 0.0702
  time to fit residues: 19.5622
Evaluate side-chains
  180 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 18 optimal weight:    8.9990
   chunk 5 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   chunk 37 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
** B  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  29 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 = 0.3410 r_free = 0.3410 target = 0.082681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.064299 restraints weight = 18776.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.066420 restraints weight = 11506.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.067691 restraints weight = 8243.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.068946 restraints weight = 6571.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.069536 restraints weight = 5481.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.5715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4770  Z= 0.131
  Angle     :  0.632  10.651   6500  Z= 0.305
  Chirality :  0.033   0.105    815
  Planarity :  0.004   0.026    770
  Dihedral  :  4.610  15.275    630
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.34), residues: 590
  helix:  0.97 (0.24), residues: 475
  sheet:  None (None), residues: 0
  loop : -3.24 (0.38), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  76 
 TYR   0.008   0.001   TYR D 132 
 PHE   0.009   0.001   PHE C  99 
 TRP   0.009   0.001   TRP D 123 
 HIS   0.013   0.003   HIS B  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 4770)
  covalent geometry    : angle       0.63230 ( 6500)
  hydrogen bonds       : bond        0.03867 (  375)
  hydrogen bonds       : angle       3.77776 ( 1125)

*********************** 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
  226 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 0.173 
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: A   44 GLN cc_start: 0.9156 (tt0) cc_final: 0.8760 (tt0)
REVERT: A   76 ARG cc_start: 0.9301 (tpp80) cc_final: 0.8912 (tpp80)
REVERT: A   94 HIS cc_start: 0.9173 (m90) cc_final: 0.8600 (m90)
REVERT: A  107 LEU cc_start: 0.9497 (mt) cc_final: 0.9179 (mt)
REVERT: B   53 LEU cc_start: 0.9007 (pt) cc_final: 0.8703 (pt)
REVERT: B   76 ARG cc_start: 0.9460 (tpp-160) cc_final: 0.9124 (mmm160)
REVERT: B   94 HIS cc_start: 0.9193 (m90) cc_final: 0.8804 (m90)
REVERT: B  107 LEU cc_start: 0.9449 (mt) cc_final: 0.9123 (mt)
REVERT: B  132 TYR cc_start: 0.8522 (t80) cc_final: 0.8271 (t80)
REVERT: B  136 ASN cc_start: 0.9049 (p0) cc_final: 0.8664 (p0)
REVERT: C   21 PHE cc_start: 0.8908 (t80) cc_final: 0.8635 (t80)
REVERT: C   76 ARG cc_start: 0.9330 (tpp80) cc_final: 0.8968 (mmm160)
REVERT: C   80 ASP cc_start: 0.8941 (t0) cc_final: 0.8332 (t0)
REVERT: C   91 LEU cc_start: 0.8678 (mp) cc_final: 0.8305 (tt)
REVERT: C   94 HIS cc_start: 0.9068 (m90) cc_final: 0.8574 (m90)
REVERT: C   97 HIS cc_start: 0.9468 (m170) cc_final: 0.9186 (m90)
REVERT: C  132 TYR cc_start: 0.8764 (t80) cc_final: 0.8475 (t80)
REVERT: D   94 HIS cc_start: 0.9247 (m90) cc_final: 0.8778 (m90)
REVERT: D   97 HIS cc_start: 0.9438 (m170) cc_final: 0.9136 (m90)
REVERT: D  136 ASN cc_start: 0.8940 (p0) cc_final: 0.8717 (p0)
REVERT: E   21 PHE cc_start: 0.9036 (t80) cc_final: 0.8669 (t80)
REVERT: E   44 GLN cc_start: 0.8983 (mt0) cc_final: 0.8380 (tt0)
REVERT: E   94 HIS cc_start: 0.9161 (m90) cc_final: 0.8738 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 226
  average time/residue: 0.0638
  time to fit residues: 18.0875
Evaluate side-chains
  179 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0570
   chunk 10 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   overall best weight:    1.3502

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.080737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.062352 restraints weight = 19023.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.064409 restraints weight = 11781.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.065865 restraints weight = 8494.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.066793 restraints weight = 6680.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.067396 restraints weight = 5676.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.6414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4770  Z= 0.128
  Angle     :  0.610  11.058   6500  Z= 0.300
  Chirality :  0.034   0.125    815
  Planarity :  0.004   0.031    770
  Dihedral  :  4.436  14.682    630
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.34), residues: 590
  helix:  1.22 (0.24), residues: 475
  sheet:  None (None), residues: 0
  loop : -3.07 (0.39), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  76 
 TYR   0.014   0.002   TYR D  70 
 PHE   0.020   0.002   PHE C  66 
 TRP   0.006   0.001   TRP D 126 
 HIS   0.012   0.002   HIS B  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 4770)
  covalent geometry    : angle       0.61021 ( 6500)
  hydrogen bonds       : bond        0.03576 (  375)
  hydrogen bonds       : angle       3.69334 ( 1125)

*********************** 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
  215 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.101 
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: 0.9470 (tpp80) cc_final: 0.9129 (tpp80)
REVERT: A   94 HIS cc_start: 0.9084 (m90) cc_final: 0.8557 (m90)
REVERT: B   76 ARG cc_start: 0.9540 (tpp-160) cc_final: 0.9132 (mmm160)
REVERT: B   79 MET cc_start: 0.9400 (tmm) cc_final: 0.9195 (tmm)
REVERT: B   80 ASP cc_start: 0.8965 (t0) cc_final: 0.8760 (t0)
REVERT: B   94 HIS cc_start: 0.9224 (m90) cc_final: 0.8837 (m90)
REVERT: B  132 TYR cc_start: 0.8563 (t80) cc_final: 0.8300 (t80)
REVERT: C   66 PHE cc_start: 0.9605 (m-80) cc_final: 0.9120 (m-80)
REVERT: C   76 ARG cc_start: 0.9390 (tpp80) cc_final: 0.8859 (tpm170)
REVERT: C   94 HIS cc_start: 0.9145 (m90) cc_final: 0.8809 (m90)
REVERT: C  102 LEU cc_start: 0.9470 (tp) cc_final: 0.9244 (mt)
REVERT: C  132 TYR cc_start: 0.8740 (t80) cc_final: 0.8429 (t80)
REVERT: D   44 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8022 (tm-30)
REVERT: D   53 LEU cc_start: 0.8884 (pt) cc_final: 0.8627 (pt)
REVERT: D   76 ARG cc_start: 0.9396 (tpp80) cc_final: 0.8960 (tpp80)
REVERT: D   94 HIS cc_start: 0.9116 (m90) cc_final: 0.8689 (m90)
REVERT: D  107 LEU cc_start: 0.9125 (mm) cc_final: 0.8797 (mm)
REVERT: E   21 PHE cc_start: 0.9105 (t80) cc_final: 0.8825 (t80)
REVERT: E   76 ARG cc_start: 0.9377 (tpp80) cc_final: 0.8967 (tpp80)
REVERT: E   94 HIS cc_start: 0.9043 (m90) cc_final: 0.8635 (m90)
REVERT: E   97 HIS cc_start: 0.9442 (m-70) cc_final: 0.9102 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.0583
  time to fit residues: 16.0099
Evaluate side-chains
  182 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 15 optimal weight:    9.9990
   chunk 31 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 27 optimal weight:    8.9990
   chunk 3 optimal weight:   10.0000
   chunk 21 optimal weight:    4.9990
   overall best weight:    1.7990

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.078654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.060391 restraints weight = 19074.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.062309 restraints weight = 12055.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.063750 restraints weight = 8784.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.064711 restraints weight = 6938.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.065252 restraints weight = 5878.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.6640

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= 0.146
  Angle     :  0.636  10.719   6500  Z= 0.313
  Chirality :  0.034   0.106    815
  Planarity :  0.004   0.031    770
  Dihedral  :  4.392  13.993    630
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.34), residues: 590
  helix:  1.29 (0.24), residues: 475
  sheet:  None (None), residues: 0
  loop : -3.01 (0.39), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  76 
 TYR   0.024   0.002   TYR B  24 
 PHE   0.020   0.002   PHE D  66 
 TRP   0.005   0.001   TRP A 126 
 HIS   0.027   0.003   HIS E  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 4770)
  covalent geometry    : angle       0.63558 ( 6500)
  hydrogen bonds       : bond        0.03599 (  375)
  hydrogen bonds       : angle       3.76751 ( 1125)

*********************** 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
  215 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.140 
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: 0.9414 (tpp80) cc_final: 0.9083 (tpp80)
REVERT: A   94 HIS cc_start: 0.8965 (m90) cc_final: 0.8386 (m90)
REVERT: B   94 HIS cc_start: 0.9115 (m90) cc_final: 0.8485 (m-70)
REVERT: B  132 TYR cc_start: 0.8530 (t80) cc_final: 0.8184 (t80)
REVERT: B  136 ASN cc_start: 0.8993 (p0) cc_final: 0.8601 (p0)
REVERT: C   66 PHE cc_start: 0.9628 (m-80) cc_final: 0.9197 (m-80)
REVERT: C   76 ARG cc_start: 0.9406 (tpp80) cc_final: 0.8851 (mmm160)
REVERT: C   94 HIS cc_start: 0.9013 (m90) cc_final: 0.8542 (m-70)
REVERT: C   97 HIS cc_start: 0.9286 (m170) cc_final: 0.9037 (m90)
REVERT: C  132 TYR cc_start: 0.8772 (t80) cc_final: 0.8404 (t80)
REVERT: C  136 ASN cc_start: 0.9032 (p0) cc_final: 0.8644 (p0)
REVERT: D   76 ARG cc_start: 0.9466 (tpp80) cc_final: 0.9102 (tpp80)
REVERT: D   94 HIS cc_start: 0.9014 (m90) cc_final: 0.8353 (m-70)
REVERT: D  107 LEU cc_start: 0.9210 (mm) cc_final: 0.8984 (mm)
REVERT: E   44 GLN cc_start: 0.8955 (tt0) cc_final: 0.8533 (tm-30)
REVERT: E   76 ARG cc_start: 0.9413 (tpp80) cc_final: 0.8996 (tpp80)
REVERT: E   94 HIS cc_start: 0.9010 (m90) cc_final: 0.8469 (m-70)
REVERT: E   97 HIS cc_start: 0.9401 (m-70) cc_final: 0.8849 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.0589
  time to fit residues: 16.1769
Evaluate side-chains
  180 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 21 optimal weight:    7.9990
   chunk 59 optimal weight:    7.9990
   chunk 20 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0970
   chunk 5 optimal weight:    2.9990
   chunk 6 optimal weight:   20.0000
   chunk 19 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 42 optimal weight:    0.4980
   overall best weight:    0.8582

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.079949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.061263 restraints weight = 18975.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.063341 restraints weight = 11854.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.064641 restraints weight = 8550.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.065833 restraints weight = 6828.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.066686 restraints weight = 5688.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.7092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   4770  Z= 0.126
  Angle     :  0.649  11.769   6500  Z= 0.309
  Chirality :  0.034   0.104    815
  Planarity :  0.004   0.032    770
  Dihedral  :  4.293  13.289    630
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.34), residues: 590
  helix:  1.38 (0.24), residues: 475
  sheet:  None (None), residues: 0
  loop : -2.83 (0.42), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  76 
 TYR   0.020   0.002   TYR D  24 
 PHE   0.017   0.002   PHE A  63 
 TRP   0.006   0.001   TRP C 123 
 HIS   0.025   0.003   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 4770)
  covalent geometry    : angle       0.64860 ( 6500)
  hydrogen bonds       : bond        0.03408 (  375)
  hydrogen bonds       : angle       3.67476 ( 1125)

*********************** 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
  224 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.107 
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   44 GLN cc_start: 0.9111 (tt0) cc_final: 0.8652 (tt0)
REVERT: A   76 ARG cc_start: 0.9397 (tpp80) cc_final: 0.9080 (tpp80)
REVERT: A   91 LEU cc_start: 0.8532 (mp) cc_final: 0.8065 (tt)
REVERT: A   94 HIS cc_start: 0.8828 (m90) cc_final: 0.8319 (m-70)
REVERT: A  136 ASN cc_start: 0.9073 (p0) cc_final: 0.8811 (p0)
REVERT: B   76 ARG cc_start: 0.9494 (tpp80) cc_final: 0.9257 (tpp80)
REVERT: B   94 HIS cc_start: 0.9006 (m90) cc_final: 0.8578 (m-70)
REVERT: B  132 TYR cc_start: 0.8497 (t80) cc_final: 0.8211 (t80)
REVERT: B  136 ASN cc_start: 0.8994 (p0) cc_final: 0.8598 (p0)
REVERT: C   62 CYS cc_start: 0.8823 (m) cc_final: 0.8449 (m)
REVERT: C   66 PHE cc_start: 0.9623 (m-80) cc_final: 0.9203 (m-80)
REVERT: C   76 ARG cc_start: 0.9363 (tpp80) cc_final: 0.8432 (mmm160)
REVERT: C   94 HIS cc_start: 0.8789 (m90) cc_final: 0.8402 (m90)
REVERT: C  132 TYR cc_start: 0.8780 (t80) cc_final: 0.8434 (t80)
REVERT: D   53 LEU cc_start: 0.8859 (pt) cc_final: 0.8612 (pt)
REVERT: D   66 PHE cc_start: 0.9558 (m-80) cc_final: 0.9168 (m-80)
REVERT: D   76 ARG cc_start: 0.9421 (tpp80) cc_final: 0.8844 (mmm160)
REVERT: D   94 HIS cc_start: 0.8838 (m90) cc_final: 0.8409 (m-70)
REVERT: E   44 GLN cc_start: 0.8948 (tt0) cc_final: 0.8691 (tm-30)
REVERT: E   76 ARG cc_start: 0.9404 (tpp80) cc_final: 0.9010 (tpp80)
REVERT: E   94 HIS cc_start: 0.8958 (m90) cc_final: 0.8530 (m-70)
REVERT: E   97 HIS cc_start: 0.9364 (m-70) cc_final: 0.8830 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 224
  average time/residue: 0.0544
  time to fit residues: 15.6061
Evaluate side-chains
  184 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0030
   chunk 1 optimal weight:    0.9990
   chunk 56 optimal weight:    8.9990
   chunk 42 optimal weight:    0.6980
   chunk 59 optimal weight:    8.9990
   chunk 39 optimal weight:    0.2980
   chunk 22 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.5992

-------------------------------------------------------------------------------
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**
A 136 ASN
** 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 = 0.3441 r_free = 0.3441 target = 0.083166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.064724 restraints weight = 18983.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.066847 restraints weight = 11868.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.068387 restraints weight = 8560.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.069491 restraints weight = 6737.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.070327 restraints weight = 5625.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.7380

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= 0.115
  Angle     :  0.640  11.750   6500  Z= 0.302
  Chirality :  0.034   0.118    815
  Planarity :  0.004   0.034    770
  Dihedral  :  4.179  12.547    630
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.76 %
    Favored  : 98.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.34), residues: 590
  helix:  1.47 (0.23), residues: 475
  sheet:  None (None), residues: 0
  loop : -2.74 (0.42), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  76 
 TYR   0.020   0.001   TYR B  24 
 PHE   0.023   0.001   PHE B  63 
 TRP   0.006   0.001   TRP A 126 
 HIS   0.016   0.003   HIS E  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 4770)
  covalent geometry    : angle       0.63963 ( 6500)
  hydrogen bonds       : bond        0.03157 (  375)
  hydrogen bonds       : angle       3.61517 ( 1125)

*********************** 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
  223 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 222
  time to evaluate  : 0.133 
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   42 LEU cc_start: 0.8942 (mm) cc_final: 0.8636 (mm)
REVERT: A   76 ARG cc_start: 0.9397 (tpp80) cc_final: 0.8793 (mmm160)
REVERT: A   94 HIS cc_start: 0.8789 (m90) cc_final: 0.8307 (m90)
REVERT: B   53 LEU cc_start: 0.8941 (pt) cc_final: 0.8648 (pt)
REVERT: B   76 ARG cc_start: 0.9467 (tpp80) cc_final: 0.9169 (tpp80)
REVERT: B   94 HIS cc_start: 0.8718 (m90) cc_final: 0.8445 (m90)
REVERT: B  132 TYR cc_start: 0.8477 (t80) cc_final: 0.8139 (t80)
REVERT: B  136 ASN cc_start: 0.8971 (p0) cc_final: 0.8600 (p0)
REVERT: C   62 CYS cc_start: 0.8719 (m) cc_final: 0.8417 (m)
REVERT: C   76 ARG cc_start: 0.9280 (tpp80) cc_final: 0.8958 (mmm160)
REVERT: C   79 MET cc_start: 0.9323 (tmm) cc_final: 0.8882 (mtp)
REVERT: C   80 ASP cc_start: 0.8960 (t0) cc_final: 0.8587 (t0)
REVERT: C   94 HIS cc_start: 0.8749 (m90) cc_final: 0.8315 (m-70)
REVERT: C  132 TYR cc_start: 0.8734 (t80) cc_final: 0.8386 (t80)
REVERT: C  136 ASN cc_start: 0.9130 (p0) cc_final: 0.8683 (p0)
REVERT: D   66 PHE cc_start: 0.9563 (m-80) cc_final: 0.9231 (m-80)
REVERT: D   76 ARG cc_start: 0.9398 (tpp80) cc_final: 0.8689 (mmm160)
REVERT: D   80 ASP cc_start: 0.9080 (t0) cc_final: 0.8850 (t0)
REVERT: D   94 HIS cc_start: 0.8739 (m90) cc_final: 0.8389 (m-70)
REVERT: E   44 GLN cc_start: 0.9052 (tt0) cc_final: 0.8681 (tm-30)
REVERT: E   76 ARG cc_start: 0.9382 (tpp80) cc_final: 0.8661 (mmm160)
REVERT: E   94 HIS cc_start: 0.8882 (m90) cc_final: 0.8414 (m-70)
  outliers start: 1
  outliers final: 1
  residues processed: 222
  average time/residue: 0.0497
  time to fit residues: 14.1815
Evaluate side-chains
  194 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 193
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 23 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 59 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 26 optimal weight:    0.2980
   chunk 5 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.7982

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.082726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.064254 restraints weight = 19301.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.066441 restraints weight = 11993.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.067997 restraints weight = 8581.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.069148 restraints weight = 6726.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.069861 restraints weight = 5593.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.7641

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= 0.118
  Angle     :  0.664  11.764   6500  Z= 0.313
  Chirality :  0.034   0.108    815
  Planarity :  0.004   0.037    770
  Dihedral  :  4.105  13.134    630
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.33), residues: 590
  helix:  1.45 (0.23), residues: 475
  sheet:  None (None), residues: 0
  loop : -2.56 (0.43), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  76 
 TYR   0.019   0.002   TYR B  70 
 PHE   0.015   0.002   PHE C  99 
 TRP   0.005   0.001   TRP A 126 
 HIS   0.029   0.003   HIS E  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 4770)
  covalent geometry    : angle       0.66407 ( 6500)
  hydrogen bonds       : bond        0.03165 (  375)
  hydrogen bonds       : angle       3.71143 ( 1125)

*********************** 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
  218 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 ARG cc_start: 0.9406 (tpp80) cc_final: 0.8792 (mmm160)
REVERT: A   94 HIS cc_start: 0.8781 (m90) cc_final: 0.8258 (m-70)
REVERT: B   53 LEU cc_start: 0.8925 (pt) cc_final: 0.8638 (pt)
REVERT: B   62 CYS cc_start: 0.8995 (m) cc_final: 0.8660 (m)
REVERT: B   66 PHE cc_start: 0.9559 (m-80) cc_final: 0.9227 (m-80)
REVERT: B   76 ARG cc_start: 0.9483 (tpp80) cc_final: 0.8834 (mmm160)
REVERT: B   94 HIS cc_start: 0.8755 (m90) cc_final: 0.8485 (m-70)
REVERT: B  132 TYR cc_start: 0.8475 (t80) cc_final: 0.8165 (t80)
REVERT: B  136 ASN cc_start: 0.8984 (p0) cc_final: 0.8617 (p0)
REVERT: C   62 CYS cc_start: 0.8731 (m) cc_final: 0.8379 (m)
REVERT: C   76 ARG cc_start: 0.9286 (tpp80) cc_final: 0.8913 (mmm160)
REVERT: C   79 MET cc_start: 0.9346 (tmm) cc_final: 0.9019 (mtp)
REVERT: C   80 ASP cc_start: 0.8967 (t0) cc_final: 0.8339 (t0)
REVERT: C   94 HIS cc_start: 0.8726 (m90) cc_final: 0.8341 (m-70)
REVERT: C  132 TYR cc_start: 0.8738 (t80) cc_final: 0.8338 (t80)
REVERT: C  136 ASN cc_start: 0.9105 (p0) cc_final: 0.8703 (p0)
REVERT: D   53 LEU cc_start: 0.8689 (pt) cc_final: 0.8442 (pt)
REVERT: D   66 PHE cc_start: 0.9557 (m-80) cc_final: 0.9211 (m-80)
REVERT: D   76 ARG cc_start: 0.9397 (tpp80) cc_final: 0.8943 (mmm160)
REVERT: D   94 HIS cc_start: 0.8738 (m90) cc_final: 0.8409 (m-70)
REVERT: E   76 ARG cc_start: 0.9466 (tpp80) cc_final: 0.8750 (mmm160)
REVERT: E   94 HIS cc_start: 0.8732 (m90) cc_final: 0.8254 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 218
  average time/residue: 0.0495
  time to fit residues: 13.9753
Evaluate side-chains
  195 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 56 optimal weight:    5.9990
   chunk 44 optimal weight:    0.6980
   chunk 27 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   chunk 50 optimal weight:    0.5980
   chunk 32 optimal weight:   10.0000
   chunk 54 optimal weight:    7.9990
   chunk 15 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 6 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    2.2586

-------------------------------------------------------------------------------
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**
** E  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.078189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.059753 restraints weight = 19568.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.061611 restraints weight = 12555.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.063050 restraints weight = 9181.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.064089 restraints weight = 7253.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.064857 restraints weight = 6102.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.7534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4770  Z= 0.173
  Angle     :  0.709  13.505   6500  Z= 0.351
  Chirality :  0.036   0.148    815
  Planarity :  0.004   0.029    770
  Dihedral  :  4.297  13.071    630
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.33), residues: 590
  helix:  1.24 (0.23), residues: 475
  sheet:  None (None), residues: 0
  loop : -2.54 (0.41), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  74 
 TYR   0.013   0.002   TYR C  70 
 PHE   0.045   0.002   PHE C  66 
 TRP   0.005   0.001   TRP C 123 
 HIS   0.028   0.003   HIS E  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 4770)
  covalent geometry    : angle       0.70872 ( 6500)
  hydrogen bonds       : bond        0.03817 (  375)
  hydrogen bonds       : angle       4.09946 ( 1125)

*********************** 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
  203 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLN cc_start: 0.9160 (tt0) cc_final: 0.8423 (tm-30)
REVERT: A   76 ARG cc_start: 0.9372 (tpp80) cc_final: 0.9044 (tpp80)
REVERT: A   94 HIS cc_start: 0.8940 (m90) cc_final: 0.8426 (m-70)
REVERT: B   62 CYS cc_start: 0.9076 (m) cc_final: 0.8778 (m)
REVERT: B   76 ARG cc_start: 0.9412 (tpp80) cc_final: 0.9067 (mmm160)
REVERT: B   79 MET cc_start: 0.9185 (tmm) cc_final: 0.8955 (mtp)
REVERT: B   80 ASP cc_start: 0.9086 (t0) cc_final: 0.8834 (t0)
REVERT: B   94 HIS cc_start: 0.8765 (m90) cc_final: 0.8429 (m-70)
REVERT: B  132 TYR cc_start: 0.8554 (t80) cc_final: 0.8212 (t80)
REVERT: B  136 ASN cc_start: 0.9042 (p0) cc_final: 0.8697 (p0)
REVERT: C   76 ARG cc_start: 0.9324 (tpp80) cc_final: 0.8911 (mmm160)
REVERT: C   77 GLU cc_start: 0.9401 (mm-30) cc_final: 0.9121 (mm-30)
REVERT: C   79 MET cc_start: 0.9294 (tmm) cc_final: 0.9019 (mtp)
REVERT: C   80 ASP cc_start: 0.9089 (t0) cc_final: 0.8557 (t0)
REVERT: C   94 HIS cc_start: 0.8953 (m90) cc_final: 0.8313 (m-70)
REVERT: C  132 TYR cc_start: 0.8760 (t80) cc_final: 0.8349 (t80)
REVERT: C  136 ASN cc_start: 0.9117 (p0) cc_final: 0.8738 (p0)
REVERT: D   76 ARG cc_start: 0.9360 (tpp80) cc_final: 0.9049 (mmm160)
REVERT: D   79 MET cc_start: 0.9286 (tmm) cc_final: 0.9048 (mtp)
REVERT: D   80 ASP cc_start: 0.9133 (t0) cc_final: 0.8605 (t0)
REVERT: D   94 HIS cc_start: 0.8894 (m90) cc_final: 0.8204 (m-70)
REVERT: E   39 ILE cc_start: 0.9470 (tp) cc_final: 0.9225 (tt)
REVERT: E   66 PHE cc_start: 0.9503 (m-10) cc_final: 0.9178 (m-80)
REVERT: E   76 ARG cc_start: 0.9405 (tpp80) cc_final: 0.9072 (tpp80)
REVERT: E   94 HIS cc_start: 0.8738 (m90) cc_final: 0.8157 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 0.0509
  time to fit residues: 13.4214
Evaluate side-chains
  179 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 3 optimal weight:    8.9990
   chunk 52 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.080599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.062401 restraints weight = 18790.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.064446 restraints weight = 11626.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.065942 restraints weight = 8321.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.066956 restraints weight = 6508.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.067681 restraints weight = 5450.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.7818

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= 0.124
  Angle     :  0.690  12.302   6500  Z= 0.325
  Chirality :  0.035   0.147    815
  Planarity :  0.004   0.030    770
  Dihedral  :  4.210  12.502    630
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.32), residues: 590
  helix:  1.26 (0.23), residues: 475
  sheet:  None (None), residues: 0
  loop : -2.43 (0.43), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  74 
 TYR   0.015   0.001   TYR B  70 
 PHE   0.036   0.002   PHE C  66 
 TRP   0.005   0.001   TRP C 123 
 HIS   0.027   0.003   HIS E  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 4770)
  covalent geometry    : angle       0.68974 ( 6500)
  hydrogen bonds       : bond        0.03329 (  375)
  hydrogen bonds       : angle       3.81217 ( 1125)

********************** 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
  216 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLN cc_start: 0.8954 (tt0) cc_final: 0.8597 (tm-30)
REVERT: A   76 ARG cc_start: 0.9403 (tpp80) cc_final: 0.9039 (mmm160)
REVERT: A   79 MET cc_start: 0.9288 (tmm) cc_final: 0.8934 (mtp)
REVERT: A   80 ASP cc_start: 0.8948 (t0) cc_final: 0.8578 (t0)
REVERT: A   94 HIS cc_start: 0.8839 (m90) cc_final: 0.8284 (m-70)
REVERT: B   53 LEU cc_start: 0.8881 (pt) cc_final: 0.8562 (pt)
REVERT: B   62 CYS cc_start: 0.9042 (m) cc_final: 0.8703 (m)
REVERT: B   66 PHE cc_start: 0.9557 (m-80) cc_final: 0.9211 (m-80)
REVERT: B   76 ARG cc_start: 0.9422 (tpp80) cc_final: 0.9167 (tpp80)
REVERT: B   94 HIS cc_start: 0.8729 (m90) cc_final: 0.8512 (m-70)
REVERT: B  132 TYR cc_start: 0.8489 (t80) cc_final: 0.8201 (t80)
REVERT: B  136 ASN cc_start: 0.8993 (p0) cc_final: 0.8640 (p0)
REVERT: C   76 ARG cc_start: 0.9357 (tpp80) cc_final: 0.8905 (mmm160)
REVERT: C   77 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9105 (mm-30)
REVERT: C   79 MET cc_start: 0.9297 (tmm) cc_final: 0.9026 (mtp)
REVERT: C   80 ASP cc_start: 0.9057 (t0) cc_final: 0.8363 (t0)
REVERT: C   94 HIS cc_start: 0.8788 (m90) cc_final: 0.8354 (m-70)
REVERT: C  132 TYR cc_start: 0.8734 (t80) cc_final: 0.8340 (t80)
REVERT: C  136 ASN cc_start: 0.9040 (p0) cc_final: 0.8648 (p0)
REVERT: D   39 ILE cc_start: 0.9496 (tp) cc_final: 0.9226 (tt)
REVERT: D   66 PHE cc_start: 0.9475 (m-80) cc_final: 0.9183 (m-80)
REVERT: D   76 ARG cc_start: 0.9345 (tpp80) cc_final: 0.8951 (mmm160)
REVERT: D   79 MET cc_start: 0.9318 (tmm) cc_final: 0.9058 (tmm)
REVERT: D   94 HIS cc_start: 0.8695 (m90) cc_final: 0.8363 (m-70)
REVERT: E   44 GLN cc_start: 0.9090 (tm-30) cc_final: 0.8883 (tm-30)
REVERT: E   66 PHE cc_start: 0.9412 (m-10) cc_final: 0.9088 (m-80)
REVERT: E   76 ARG cc_start: 0.9507 (tpp80) cc_final: 0.9190 (tpp-160)
REVERT: E   94 HIS cc_start: 0.8626 (m90) cc_final: 0.8027 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 216
  average time/residue: 0.0499
  time to fit residues: 13.9698
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  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0670
   chunk 28 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 59 optimal weight:   10.0000
   chunk 23 optimal weight:    0.0070
   chunk 6 optimal weight:    0.0050
   chunk 3 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.3752

-------------------------------------------------------------------------------
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 = 0.3477 r_free = 0.3477 target = 0.084372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.065698 restraints weight = 18780.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.067836 restraints weight = 11789.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.069338 restraints weight = 8490.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.070541 restraints weight = 6763.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.071197 restraints weight = 5616.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.8057

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= 0.120
  Angle     :  0.681  12.346   6500  Z= 0.318
  Chirality :  0.035   0.170    815
  Planarity :  0.004   0.031    770
  Dihedral  :  4.116  12.380    630
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.33), residues: 590
  helix:  1.33 (0.23), residues: 475
  sheet:  None (None), residues: 0
  loop : -2.40 (0.44), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  76 
 TYR   0.018   0.001   TYR B  24 
 PHE   0.031   0.002   PHE C  66 
 TRP   0.005   0.001   TRP C 126 
 HIS   0.010   0.002   HIS D  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 4770)
  covalent geometry    : angle       0.68088 ( 6500)
  hydrogen bonds       : bond        0.03074 (  375)
  hydrogen bonds       : angle       3.67737 ( 1125)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 822.30 seconds
wall clock time: 14 minutes 50.90 seconds (890.90 seconds total)