Starting phenix.real_space_refine
on Tue Feb  3 14:22:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mni_48424/02_2026/9mni_48424.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mni_48424/02_2026/9mni_48424.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mni_48424/02_2026/9mni_48424.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mni_48424/02_2026/9mni_48424.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mni_48424/02_2026/9mni_48424.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mni_48424/02_2026/9mni_48424.map"
  }
  resolution = 4.06
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.016
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      26      5.16       5
     C    2382      2.51       5
     N     599      2.21       5
     O     597      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3604
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "E"
      Number of atoms: 721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 721
          Classifications: {'peptide': 112}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105}
          Unresolved non-hydrogen bonds: 194
          Unresolved non-hydrogen angles: 250
          Unresolved non-hydrogen dihedrals: 164
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 7, 'GLU:plan': 6, 'GLN:plan1': 2, 'ASP:plan': 4, 'TRP:plan': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 133
    Chain: "R"
      Number of atoms: 2478
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2478
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 84}
          Link IDs: {'PTRANS': 9, 'TRANS': 328}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 307
          Unresolved non-hydrogen angles: 391
          Unresolved non-hydrogen dihedrals: 251
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 6, 'ASN:plan1': 13, 'GLU:plan': 7, 'TYR:plan': 4, 'ASP:plan': 6, 'TRP:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 194
    Chain: "A"
      Number of atoms: 405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 405
          Classifications: {'peptide': 66}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'TRANS': 65}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 136
          Unresolved non-hydrogen angles: 167
          Unresolved non-hydrogen dihedrals: 111
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 8, 'GLN:plan1': 1, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 74
  Time building chain proxies: 1.04, per 1000 atoms: 0.29
  Number of scatterers: 3604
  At special positions: 0
  Unit cell: (60.2, 64.5, 108.36, 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      26     16.00
     O     597      8.00
     N     599      7.00
     C    2382      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  40 " - pdb=" SG  CYS E  72 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  57 " - pdb=" SG  CYS E 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  48 " - pdb=" SG  CYS R  74 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  65 " - pdb=" SG  CYS R 105 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  88 " - pdb=" SG  CYS R 127 " distance=2.05
    Simple disulfide: pdb=" SG  CYS R 212 " - pdb=" SG  CYS R 282 " distance=2.04

  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: 0.19
  Conformation dependent library (CDL) restraints added in 93.9 milliseconds
  

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  984

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 3 sheets defined
      78.1% alpha, 2.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'E' and resid 31 through 49
      removed outlier: 3.811A  pdb=" N   VAL E  46 " --> pdb=" O   THR E  42 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   ASP E  47 " --> pdb=" O   GLN E  43 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 58 through 81
      removed outlier: 4.691A  pdb=" N   ARG E  64 " --> pdb=" O   GLY E  60 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   SER E  65 " --> pdb=" O   ARG E  61 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   GLU E  68 " --> pdb=" O   ARG E  64 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 88 through 100
    Processing helix  chain 'E' and resid 101 through 104
      removed outlier: 4.295A  pdb=" N   CYS E 104 " --> pdb=" O   PHE E 101 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 101 through 104'
    Processing helix  chain 'E' and resid 115 through 118
      removed outlier: 3.667A  pdb=" N   ILE E 118 " --> pdb=" O   PRO E 115 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 115 through 118'
    Processing helix  chain 'E' and resid 119 through 140
      removed outlier: 3.733A  pdb=" N   ILE E 123 " --> pdb=" O   LEU E 119 " (cutoff:3.500A)
      Proline residue:  E 126  - end of helix
    Processing helix  chain 'R' and resid 33 through 36
      removed outlier: 3.936A  pdb=" N   VAL R  36 " --> pdb=" O   GLN R  33 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 33 through 36'
    Processing helix  chain 'R' and resid 37 through 54
    Processing helix  chain 'R' and resid 131 through 166
      removed outlier: 3.836A  pdb=" N   VAL R 135 " --> pdb=" O   THR R 131 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 167 through 170
    Processing helix  chain 'R' and resid 171 through 196
    Processing helix  chain 'R' and resid 201 through 207
      removed outlier: 3.592A  pdb=" N   VAL R 205 " --> pdb=" O   ASN R 201 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   THR R 207 " --> pdb=" O   ALA R 203 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 209 through 243
      removed outlier: 3.828A  pdb=" N   LYS R 213 " --> pdb=" O   PRO R 209 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLN R 216 " --> pdb=" O   CYS R 212 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   TYR R 227 " --> pdb=" O   MET R 223 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY R 234 " --> pdb=" O   MET R 230 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   VAL R 243 " --> pdb=" O   THR R 239 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 252 through 261
    Processing helix  chain 'R' and resid 263 through 277
    Processing helix  chain 'R' and resid 280 through 284
      removed outlier: 3.799A  pdb=" N   ILE R 284 " --> pdb=" O   ASN R 281 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 288 through 290
      No H-bonds generated for 'chain 'R' and resid 288 through 290'
    Processing helix  chain 'R' and resid 291 through 318
      Proline residue:  R 297  - end of helix
    Processing helix  chain 'R' and resid 330 through 347
      Proline residue:  R 343  - end of helix
    Processing helix  chain 'R' and resid 347 through 352
    Processing helix  chain 'R' and resid 364 through 375
    Processing helix  chain 'R' and resid 375 through 386
    Processing helix  chain 'R' and resid 388 through 402
      removed outlier: 3.502A  pdb=" N   GLN R 401 " --> pdb=" O   ARG R 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2 through 20
    Processing helix  chain 'A' and resid 22 through 39
    Processing helix  chain 'A' and resid 43 through 68
    Processing sheet with id=AA1, first strand: chain 'R' and resid 68 through 69
    Processing sheet with id=AA2, first strand: chain 'R' and resid 82 through 87
    Processing sheet with id=AA3, first strand: chain 'R' and resid 113 through 114
      removed outlier: 3.591A  pdb=" N   ARG R 119 " --> pdb=" O   HIS R 114 " (cutoff:3.500A)

    286 hydrogen bonds defined for protein.
    846 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: 0.35

  Time building geometry restraints manager: 0.26 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1119
        1.35 -     1.47: 1028
        1.47 -     1.59: 1515
        1.59 -     1.71: 0
        1.71 -     1.84: 35
  Bond restraints: 3697
  Sorted by residual:
  bond pdb=" N   ASN A   1 "
       pdb=" CA  ASN A   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.89e+00
  bond pdb=" CA  GLU E  38 "
       pdb=" C   GLU E  38 "
    ideal  model  delta    sigma   weight residual
    1.524  1.502  0.021 1.37e-02 5.33e+03 2.44e+00
  bond pdb=" N   THR E  42 "
       pdb=" CA  THR E  42 "
    ideal  model  delta    sigma   weight residual
    1.459  1.441  0.018 1.20e-02 6.94e+03 2.34e+00
  bond pdb=" CG1 ILE R  41 "
       pdb=" CD1 ILE R  41 "
    ideal  model  delta    sigma   weight residual
    1.513  1.455  0.058 3.90e-02 6.57e+02 2.20e+00
  bond pdb=" N   GLY E 116 "
       pdb=" CA  GLY E 116 "
    ideal  model  delta    sigma   weight residual
    1.449  1.470 -0.021 1.45e-02 4.76e+03 2.06e+00
  ... (remaining 3692 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 4862
        1.86 -     3.72: 187
        3.72 -     5.58: 20
        5.58 -     7.44: 9
        7.44 -     9.31: 2
  Bond angle restraints: 5080
  Sorted by residual:
  angle pdb=" N   VAL R 198 "
        pdb=" CA  VAL R 198 "
        pdb=" C   VAL R 198 "
      ideal   model   delta    sigma   weight residual
     113.53  107.61    5.92 9.80e-01 1.04e+00 3.65e+01
  angle pdb=" C   LYS E  79 "
        pdb=" N   LEU E  80 "
        pdb=" CA  LEU E  80 "
      ideal   model   delta    sigma   weight residual
     120.28  128.84   -8.56 1.44e+00 4.82e-01 3.53e+01
  angle pdb=" N   LEU E  41 "
        pdb=" CA  LEU E  41 "
        pdb=" C   LEU E  41 "
      ideal   model   delta    sigma   weight residual
     113.41  106.27    7.14 1.22e+00 6.72e-01 3.42e+01
  angle pdb=" C   PHE E  83 "
        pdb=" N   TRP E  84 "
        pdb=" CA  TRP E  84 "
      ideal   model   delta    sigma   weight residual
     121.57  112.26    9.31 1.62e+00 3.81e-01 3.30e+01
  angle pdb=" N   VAL E 125 "
        pdb=" CA  VAL E 125 "
        pdb=" C   VAL E 125 "
      ideal   model   delta    sigma   weight residual
     112.35  106.48    5.87 1.20e+00 6.94e-01 2.39e+01
  ... (remaining 5075 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.29: 1918
       14.29 -    28.57: 134
       28.57 -    42.86: 32
       42.86 -    57.15: 7
       57.15 -    71.43: 3
  Dihedral angle restraints: 2094
    sinusoidal: 581
      harmonic: 1513
  Sorted by residual:
  dihedral pdb=" CB  CYS R  88 "
           pdb=" SG  CYS R  88 "
           pdb=" SG  CYS R 127 "
           pdb=" CB  CYS R 127 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   43.78   49.22     1      1.00e+01 1.00e-02 3.33e+01
  dihedral pdb=" CB  CYS E  57 "
           pdb=" SG  CYS E  57 "
           pdb=" SG  CYS E 104 "
           pdb=" CB  CYS E 104 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   44.55   48.45     1      1.00e+01 1.00e-02 3.23e+01
  dihedral pdb=" CB  CYS R 212 "
           pdb=" SG  CYS R 212 "
           pdb=" SG  CYS R 282 "
           pdb=" CB  CYS R 282 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  127.32  -34.32     1      1.00e+01 1.00e-02 1.67e+01
  ... (remaining 2091 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 414
       0.039 -    0.078: 140
       0.078 -    0.118: 49
       0.118 -    0.157: 10
       0.157 -    0.196: 2
  Chirality restraints: 615
  Sorted by residual:
  chirality pdb=" CA  LEU E  80 "
            pdb=" N   LEU E  80 "
            pdb=" C   LEU E  80 "
            pdb=" CB  LEU E  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.60e-01
  chirality pdb=" CA  HIS R 374 "
            pdb=" N   HIS R 374 "
            pdb=" C   HIS R 374 "
            pdb=" CB  HIS R 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.28e-01
  chirality pdb=" CA  ILE E 106 "
            pdb=" N   ILE E 106 "
            pdb=" C   ILE E 106 "
            pdb=" CB  ILE E 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.40e-01
  ... (remaining 612 not shown)

  Planarity restraints: 629
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E  37 "    0.035 2.00e-02 2.50e+03   6.96e-02 4.84e+01
        pdb=" C   ARG E  37 "   -0.120 2.00e-02 2.50e+03
        pdb=" O   ARG E  37 "    0.045 2.00e-02 2.50e+03
        pdb=" N   GLU E  38 "    0.040 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS E  40 "   -0.025 2.00e-02 2.50e+03   4.87e-02 2.37e+01
        pdb=" C   CYS E  40 "    0.084 2.00e-02 2.50e+03
        pdb=" O   CYS E  40 "   -0.031 2.00e-02 2.50e+03
        pdb=" N   LEU E  41 "   -0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E  39 "   -0.018 2.00e-02 2.50e+03   3.65e-02 1.33e+01
        pdb=" C   LEU E  39 "    0.063 2.00e-02 2.50e+03
        pdb=" O   LEU E  39 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   CYS E  40 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 626 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.93: 1615
        2.93 -     3.42: 3901
        3.42 -     3.91: 5669
        3.91 -     4.41: 6279
        4.41 -     4.90: 10123
  Nonbonded interactions: 27587
  Sorted by model distance:
  nonbonded pdb=" O   LEU R 240 "
            pdb=" O   ALA R 244 "
     model   vdw
     2.434 3.040
  nonbonded pdb=" OD1 ASP E 113 "
            pdb=" OG1 THR R 288 "
     model   vdw
     2.562 3.040
  nonbonded pdb=" O   SER E 141 "
            pdb=" OG  SER E 141 "
     model   vdw
     2.568 3.040
  nonbonded pdb=" O   TRP R  72 "
            pdb=" OH  TYR R  91 "
     model   vdw
     2.569 3.040
  nonbonded pdb=" O   PHE E  83 "
            pdb=" CA  TRP E  84 "
     model   vdw
     2.578 2.776
  ... (remaining 27582 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.00 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:             1.240
  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:                    0.010
  Process input model:                     4.460
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6125
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      :  0.004   0.058   3703  Z= 0.210
  Angle     :  0.865   9.305   5092  Z= 0.565
  Chirality :  0.046   0.196    615
  Planarity :  0.007   0.070    629
  Dihedral  : 11.047  71.432   1092
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 are not related in a simple way.
  whole:  1.28 (0.39), residues: 498
  helix:  1.60 (0.28), residues: 342
  sheet: -0.81 (1.02), residues: 21
  loop : -0.75 (0.56), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.002   ARG E  64 
 TYR   0.018   0.001   TYR R 236 
 PHE   0.026   0.002   PHE E  83 
 TRP   0.023   0.002   TRP R  72 
 HIS   0.008   0.002   HIS R 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 3697)
  covalent geometry    : angle       0.85946 ( 5080)
  SS BOND              : bond        0.00916 (    6)
  SS BOND              : angle       2.23591 (   12)
  hydrogen bonds       : bond        0.16321 (  286)
  hydrogen bonds       : angle       6.15915 (  846)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
REVERT: R   52 ILE cc_start: 0.5234 (mm) cc_final: 0.4894 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.0287
  time to fit residues: 2.8847
Evaluate side-chains
  49 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0030
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.4980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.4990

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

Flipped N/Q/H residues before XYZ refinement:
R 114 HIS
R 187 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4882 r_free = 0.4882 target = 0.266094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.206356 restraints weight = 3283.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.211879 restraints weight = 2281.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.214681 restraints weight = 1764.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.217529 restraints weight = 1476.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.218459 restraints weight = 1292.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.4510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6342
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3703  Z= 0.146
  Angle     :  0.602   7.416   5092  Z= 0.323
  Chirality :  0.039   0.173    615
  Planarity :  0.004   0.041    629
  Dihedral  :  4.402  15.535    536
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  3.48 %
    Favored  : 96.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 are not related in a simple way.
  whole:  1.60 (0.37), residues: 498
  helix:  1.84 (0.27), residues: 357
  sheet:  0.84 (1.44), residues: 12
  loop : -1.14 (0.54), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E  67 
 TYR   0.013   0.001   TYR A  29 
 PHE   0.023   0.002   PHE E  44 
 TRP   0.017   0.002   TRP E  74 
 HIS   0.005   0.001   HIS R 270 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 3697)
  covalent geometry    : angle       0.59853 ( 5080)
  SS BOND              : bond        0.00337 (    6)
  SS BOND              : angle       1.52997 (   12)
  hydrogen bonds       : bond        0.04474 (  286)
  hydrogen bonds       : angle       3.87487 (  846)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 0.079 
Fit side-chains
   revert: symmetry clash
REVERT: E   48 MET cc_start: 0.7142 (mpp) cc_final: 0.6861 (mpp)
REVERT: R   52 ILE cc_start: 0.5144 (mm) cc_final: 0.4801 (mt)
REVERT: R  217 PHE cc_start: 0.6888 (t80) cc_final: 0.6579 (t80)
REVERT: R  373 MET cc_start: 0.6617 (mtp) cc_final: 0.6052 (ttm)
  outliers start: 1
  outliers final: 0
  residues processed: 63
  average time/residue: 0.0324
  time to fit residues: 2.7660
Evaluate side-chains
  51 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 47 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0770
   chunk 5 optimal weight:    4.9990
   chunk 39 optimal weight:    0.5980
   chunk 7 optimal weight:    8.9990
   chunk 31 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
R 187 ASN
R 219 HIS
A  52 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4901 r_free = 0.4901 target = 0.268840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.210037 restraints weight = 3260.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.214578 restraints weight = 2259.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.219418 restraints weight = 1720.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4541 r_free = 0.4541 target = 0.221004 restraints weight = 1353.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.222418 restraints weight = 1165.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.4530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6399
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3703  Z= 0.137
  Angle     :  0.564   6.112   5092  Z= 0.298
  Chirality :  0.038   0.152    615
  Planarity :  0.004   0.034    629
  Dihedral  :  4.318  20.190    536
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 are not related in a simple way.
  whole:  2.03 (0.38), residues: 498
  helix:  2.17 (0.27), residues: 358
  sheet:  1.28 (1.40), residues: 12
  loop : -1.08 (0.54), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E  64 
 TYR   0.017   0.001   TYR R 236 
 PHE   0.052   0.002   PHE E  44 
 TRP   0.018   0.001   TRP E  74 
 HIS   0.004   0.001   HIS R 270 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3697)
  covalent geometry    : angle       0.56259 ( 5080)
  SS BOND              : bond        0.00516 (    6)
  SS BOND              : angle       0.91294 (   12)
  hydrogen bonds       : bond        0.03871 (  286)
  hydrogen bonds       : angle       3.54101 (  846)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
REVERT: R   52 ILE cc_start: 0.4789 (mm) cc_final: 0.4420 (mt)
REVERT: R  373 MET cc_start: 0.6774 (mtp) cc_final: 0.5932 (ttm)
REVERT: A   12 MET cc_start: 0.7963 (mmm) cc_final: 0.7691 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.0409
  time to fit residues: 3.5058
Evaluate side-chains
  50 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0070
   chunk 2 optimal weight:    0.3980
   chunk 28 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 17 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
R 187 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4878 r_free = 0.4878 target = 0.274498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.220470 restraints weight = 3482.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.224323 restraints weight = 2635.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.227339 restraints weight = 2108.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.229025 restraints weight = 1793.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.230257 restraints weight = 1595.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.4523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6391
moved from start:          0.3220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3703  Z= 0.125
  Angle     :  0.540   6.897   5092  Z= 0.285
  Chirality :  0.038   0.134    615
  Planarity :  0.004   0.031    629
  Dihedral  :  4.205  21.623    536
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 are not related in a simple way.
  whole:  2.27 (0.38), residues: 498
  helix:  2.39 (0.27), residues: 358
  sheet:  1.51 (1.55), residues: 12
  loop : -1.16 (0.53), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  64 
 TYR   0.017   0.001   TYR R 236 
 PHE   0.035   0.002   PHE E  44 
 TRP   0.017   0.001   TRP E  74 
 HIS   0.003   0.001   HIS R 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 3697)
  covalent geometry    : angle       0.53881 ( 5080)
  SS BOND              : bond        0.00631 (    6)
  SS BOND              : angle       0.83456 (   12)
  hydrogen bonds       : bond        0.03528 (  286)
  hydrogen bonds       : angle       3.45460 (  846)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
REVERT: R   52 ILE cc_start: 0.4583 (mm) cc_final: 0.4166 (mt)
REVERT: R  373 MET cc_start: 0.6765 (mtp) cc_final: 0.5990 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.0584
  time to fit residues: 4.5419
Evaluate side-chains
  46 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 24 optimal weight:    0.2980
   chunk 33 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 49 optimal weight:    9.9990
   chunk 22 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 27 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
R 187 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4742 r_free = 0.4742 target = 0.252135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 94)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.192858 restraints weight = 3243.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.196418 restraints weight = 2646.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.197768 restraints weight = 2256.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.198964 restraints weight = 2024.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.199965 restraints weight = 1866.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.4310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6502
moved from start:          0.3503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3703  Z= 0.141
  Angle     :  0.577   7.010   5092  Z= 0.302
  Chirality :  0.039   0.148    615
  Planarity :  0.004   0.030    629
  Dihedral  :  4.253  23.579    536
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 are not related in a simple way.
  whole:  2.27 (0.39), residues: 498
  helix:  2.38 (0.28), residues: 358
  sheet:  1.73 (1.55), residues: 12
  loop : -1.14 (0.53), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  64 
 TYR   0.018   0.001   TYR R 236 
 PHE   0.030   0.002   PHE E  44 
 TRP   0.023   0.002   TRP E  74 
 HIS   0.005   0.001   HIS R 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3697)
  covalent geometry    : angle       0.57539 ( 5080)
  SS BOND              : bond        0.00257 (    6)
  SS BOND              : angle       0.95265 (   12)
  hydrogen bonds       : bond        0.03579 (  286)
  hydrogen bonds       : angle       3.49929 (  846)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   52 ILE cc_start: 0.4440 (mm) cc_final: 0.4130 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.0445
  time to fit residues: 3.7358
Evaluate side-chains
  50 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 22 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 14 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   chunk 23 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 226 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4742 r_free = 0.4742 target = 0.252164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.192571 restraints weight = 3237.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.195852 restraints weight = 2526.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.198704 restraints weight = 2120.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.199224 restraints weight = 1862.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.200189 restraints weight = 1777.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.4329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6480
moved from start:          0.3782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3703  Z= 0.143
  Angle     :  0.569   7.455   5092  Z= 0.298
  Chirality :  0.039   0.133    615
  Planarity :  0.004   0.030    629
  Dihedral  :  4.209  24.606    536
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 are not related in a simple way.
  whole:  2.22 (0.39), residues: 498
  helix:  2.31 (0.28), residues: 358
  sheet:  2.17 (1.61), residues: 12
  loop : -1.13 (0.53), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E  67 
 TYR   0.017   0.001   TYR R 236 
 PHE   0.023   0.002   PHE R 184 
 TRP   0.015   0.001   TRP E  74 
 HIS   0.007   0.002   HIS R 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3697)
  covalent geometry    : angle       0.56839 ( 5080)
  SS BOND              : bond        0.00278 (    6)
  SS BOND              : angle       0.91872 (   12)
  hydrogen bonds       : bond        0.03495 (  286)
  hydrogen bonds       : angle       3.51679 (  846)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   52 ILE cc_start: 0.4482 (mm) cc_final: 0.4145 (mt)
REVERT: R  239 THR cc_start: 0.8395 (m) cc_final: 0.8168 (m)
REVERT: R  373 MET cc_start: 0.6694 (mtp) cc_final: 0.5894 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0489
  time to fit residues: 4.4612
Evaluate side-chains
  53 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 47 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A  20 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4626 r_free = 0.4626 target = 0.234850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.172806 restraints weight = 3508.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.176564 restraints weight = 2685.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.178394 restraints weight = 2228.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.180081 restraints weight = 1968.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.181805 restraints weight = 1807.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.4187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6594
moved from start:          0.4058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3703  Z= 0.170
  Angle     :  0.618   7.302   5092  Z= 0.326
  Chirality :  0.042   0.147    615
  Planarity :  0.004   0.031    629
  Dihedral  :  4.454  27.142    536
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 are not related in a simple way.
  whole:  1.85 (0.38), residues: 498
  helix:  2.06 (0.28), residues: 358
  sheet:  1.28 (1.63), residues: 14
  loop : -1.30 (0.52), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 314 
 TYR   0.022   0.001   TYR R 236 
 PHE   0.021   0.002   PHE E  44 
 TRP   0.017   0.002   TRP R 254 
 HIS   0.007   0.002   HIS R 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 3697)
  covalent geometry    : angle       0.61778 ( 5080)
  SS BOND              : bond        0.00324 (    6)
  SS BOND              : angle       0.83113 (   12)
  hydrogen bonds       : bond        0.03836 (  286)
  hydrogen bonds       : angle       3.71960 (  846)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   52 ILE cc_start: 0.4378 (mm) cc_final: 0.4057 (mt)
REVERT: R  373 MET cc_start: 0.6799 (mtp) cc_final: 0.5871 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0362
  time to fit residues: 3.3152
Evaluate side-chains
  55 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 18 optimal weight:   10.0000
   chunk 39 optimal weight:    0.7980
   chunk 15 optimal weight:    8.9990
   chunk 9 optimal weight:    0.0170
   chunk 33 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    9.9990
   chunk 8 optimal weight:   20.0000
   overall best weight:    0.7618

-------------------------------------------------------------------------------
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 = 0.4648 r_free = 0.4648 target = 0.238156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.177958 restraints weight = 3424.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.181390 restraints weight = 2556.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.184641 restraints weight = 2101.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.186256 restraints weight = 1827.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.187249 restraints weight = 1652.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.4234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6531
moved from start:          0.4229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3703  Z= 0.143
  Angle     :  0.583   7.425   5092  Z= 0.309
  Chirality :  0.039   0.132    615
  Planarity :  0.004   0.032    629
  Dihedral  :  4.340  23.774    536
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 are not related in a simple way.
  whole:  2.01 (0.38), residues: 498
  helix:  2.19 (0.28), residues: 359
  sheet:  1.25 (1.64), residues: 14
  loop : -1.29 (0.52), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 314 
 TYR   0.016   0.001   TYR R 236 
 PHE   0.030   0.002   PHE R 184 
 TRP   0.011   0.001   TRP E  74 
 HIS   0.005   0.001   HIS R 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 3697)
  covalent geometry    : angle       0.58271 ( 5080)
  SS BOND              : bond        0.00240 (    6)
  SS BOND              : angle       0.80485 (   12)
  hydrogen bonds       : bond        0.03533 (  286)
  hydrogen bonds       : angle       3.62852 (  846)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: R   52 ILE cc_start: 0.4491 (mm) cc_final: 0.4199 (mt)
REVERT: R  373 MET cc_start: 0.6678 (mtp) cc_final: 0.5971 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.0449
  time to fit residues: 3.7800
Evaluate side-chains
  51 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 27 optimal weight:    0.0970
   chunk 13 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 1 optimal weight:    8.9990
   chunk 6 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 49 optimal weight:    9.9990
   chunk 11 optimal weight:    4.9990
   chunk 39 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0980
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
R 374 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.242982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.182594 restraints weight = 3354.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.187000 restraints weight = 2485.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.189523 restraints weight = 1996.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.191773 restraints weight = 1718.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.192747 restraints weight = 1543.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.4278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6441
moved from start:          0.4358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3703  Z= 0.117
  Angle     :  0.541   7.710   5092  Z= 0.286
  Chirality :  0.038   0.127    615
  Planarity :  0.004   0.033    629
  Dihedral  :  4.070  23.494    536
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 are not related in a simple way.
  whole:  2.21 (0.39), residues: 498
  helix:  2.36 (0.27), residues: 359
  sheet:  1.16 (1.63), residues: 14
  loop : -1.28 (0.54), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 314 
 TYR   0.011   0.001   TYR R 236 
 PHE   0.045   0.002   PHE E  44 
 TRP   0.010   0.001   TRP E  84 
 HIS   0.006   0.001   HIS R 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 3697)
  covalent geometry    : angle       0.54018 ( 5080)
  SS BOND              : bond        0.00183 (    6)
  SS BOND              : angle       0.72011 (   12)
  hydrogen bonds       : bond        0.03326 (  286)
  hydrogen bonds       : angle       3.50659 (  846)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   48 MET cc_start: 0.7659 (mpp) cc_final: 0.7315 (mpp)
REVERT: R   52 ILE cc_start: 0.4466 (mm) cc_final: 0.4196 (mt)
REVERT: R  373 MET cc_start: 0.6861 (mtp) cc_final: 0.5846 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0421
  time to fit residues: 3.2088
Evaluate side-chains
  47 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 8 optimal weight:    9.9990
   chunk 6 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   chunk 36 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.4642 r_free = 0.4642 target = 0.237148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.177799 restraints weight = 3506.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.181360 restraints weight = 2709.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.183582 restraints weight = 2212.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.185020 restraints weight = 1918.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.186453 restraints weight = 1742.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.4229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6538
moved from start:          0.4544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3703  Z= 0.145
  Angle     :  0.588   7.725   5092  Z= 0.311
  Chirality :  0.040   0.153    615
  Planarity :  0.004   0.031    629
  Dihedral  :  4.292  27.461    536
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 are not related in a simple way.
  whole:  1.98 (0.39), residues: 498
  helix:  2.17 (0.28), residues: 359
  sheet:  1.15 (1.67), residues: 14
  loop : -1.33 (0.53), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 314 
 TYR   0.019   0.001   TYR R 236 
 PHE   0.030   0.002   PHE E  44 
 TRP   0.018   0.001   TRP E  74 
 HIS   0.006   0.001   HIS R 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 3697)
  covalent geometry    : angle       0.58786 ( 5080)
  SS BOND              : bond        0.00254 (    6)
  SS BOND              : angle       0.71882 (   12)
  hydrogen bonds       : bond        0.03586 (  286)
  hydrogen bonds       : angle       3.62202 (  846)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   48 MET cc_start: 0.7600 (mpp) cc_final: 0.7314 (mpp)
REVERT: R   52 ILE cc_start: 0.4456 (mm) cc_final: 0.4138 (mt)
REVERT: R  373 MET cc_start: 0.7231 (mtp) cc_final: 0.7007 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0540
  time to fit residues: 4.1360
Evaluate side-chains
  51 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 34 optimal weight:    0.3980
   chunk 21 optimal weight:    0.9990
   chunk 1 optimal weight:    5.9990
   chunk 12 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 44 optimal weight:    0.2980
   chunk 49 optimal weight:   10.0000
   chunk 28 optimal weight:    0.8980
   chunk 48 optimal weight:    8.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4659 r_free = 0.4659 target = 0.239922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.181566 restraints weight = 3423.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.185792 restraints weight = 2520.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.188185 restraints weight = 2054.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.190023 restraints weight = 1780.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.190728 restraints weight = 1599.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.4260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6472
moved from start:          0.4603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3703  Z= 0.123
  Angle     :  0.544   7.732   5092  Z= 0.286
  Chirality :  0.038   0.126    615
  Planarity :  0.004   0.033    629
  Dihedral  :  4.074  24.529    536
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 are not related in a simple way.
  whole:  2.13 (0.39), residues: 498
  helix:  2.29 (0.28), residues: 359
  sheet:  0.96 (1.62), residues: 14
  loop : -1.26 (0.54), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  46 
 TYR   0.013   0.001   TYR R 236 
 PHE   0.023   0.002   PHE E  44 
 TRP   0.014   0.001   TRP E  74 
 HIS   0.003   0.001   HIS R 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 3697)
  covalent geometry    : angle       0.54410 ( 5080)
  SS BOND              : bond        0.00225 (    6)
  SS BOND              : angle       0.68259 (   12)
  hydrogen bonds       : bond        0.03235 (  286)
  hydrogen bonds       : angle       3.54164 (  846)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 738.69 seconds
wall clock time: 13 minutes 19.68 seconds (799.68 seconds total)