Starting phenix.real_space_refine
on Tue Mar  3 10:49:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggr_40018/03_2026/8ggr_40018.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggr_40018/03_2026/8ggr_40018.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ggr_40018/03_2026/8ggr_40018.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggr_40018/03_2026/8ggr_40018.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggr_40018/03_2026/8ggr_40018.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggr_40018/03_2026/8ggr_40018.cif"
  }
  resolution = 3.4
  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=   0.025
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      16      5.16       5
     C    1434      2.51       5
     N     335      2.21       5
     O     358      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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2143
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2127
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2127
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 135
          Unresolved non-hydrogen angles: 166
          Unresolved non-hydrogen dihedrals: 113
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 7, 'ASP:plan': 4, 'ARG:plan': 5, 'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 90
    Chain: "R"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 16
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 0.76, per 1000 atoms: 0.35
  Number of scatterers: 2143
  At special positions: 0
  Unit cell: (55.5328, 85.0346, 62.4744, 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      16     16.00
     O     358      8.00
     N     335      7.00
     C    1434      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03

  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: 0.27
  Conformation dependent library (CDL) restraints added in 83.1 milliseconds
  

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  538

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 0 sheets defined
      89.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 3.779A  pdb=" N   GLY R  37 " --> pdb=" O   VAL R  33 " (cutoff:3.500A)
      removed outlier: 5.797A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   MET R  40 " --> pdb=" O   MET R  36 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 62 through 65
    Processing helix  chain 'R' and resid 68 through 97
      removed outlier: 3.998A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.849A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 3.505A  pdb=" N   SER R 137 " --> pdb=" O   PHE R 133 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
      removed outlier: 3.502A  pdb=" N   LEU R 145 " --> pdb=" O   TYR R 141 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.508A  pdb=" N   ALA R 150 " --> pdb=" O   THR R 146 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   SER R 165 " --> pdb=" O   SER R 161 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
      removed outlier: 3.635A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 237
    Processing helix  chain 'R' and resid 270 through 299
      removed outlier: 4.078A  pdb=" N   THR R 274 " --> pdb=" O   LYS R 270 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ILE R 278 " --> pdb=" O   THR R 274 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.616A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   ILE R 298 " --> pdb=" O   ILE R 294 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.810A  pdb=" N   TYR R 308 " --> pdb=" O   ARG R 304 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ILE R 309 " --> pdb=" O   LYS R 305 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 317 through 327
      removed outlier: 3.652A  pdb=" N   PHE R 321 " --> pdb=" O   VAL R 317 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ASN R 322 " --> pdb=" O   ASN R 318 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 340

    163 hydrogen bonds defined for protein.
    486 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: 0.26

  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: 633
        1.35 -     1.46: 570
        1.46 -     1.58: 972
        1.58 -     1.70: 0
        1.70 -     1.81: 23
  Bond restraints: 2198
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.450 -0.053 2.00e-02 2.50e+03 6.91e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.572 -0.049 2.00e-02 2.50e+03 5.97e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.565 -0.045 2.00e-02 2.50e+03 5.02e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.438 -0.044 2.00e-02 2.50e+03 4.91e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" OAK G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.353  1.322  0.031 2.00e-02 2.50e+03 2.38e+00
  ... (remaining 2193 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.12: 2901
        1.12 -     2.24: 82
        2.24 -     3.36: 19
        3.36 -     4.48: 4
        4.48 -     5.60: 7
  Bond angle restraints: 3013
  Sorted by residual:
  angle pdb=" CAG G1I R 501 "
        pdb=" CAH G1I R 501 "
        pdb=" CAI G1I R 501 "
      ideal   model   delta    sigma   weight residual
     110.89  116.49   -5.60 3.00e+00 1.11e-01 3.49e+00
  angle pdb=" CAE G1I R 501 "
        pdb=" CAG G1I R 501 "
        pdb=" CAH G1I R 501 "
      ideal   model   delta    sigma   weight residual
     112.63  118.21   -5.58 3.00e+00 1.11e-01 3.46e+00
  angle pdb=" N   ILE R  94 "
        pdb=" CA  ILE R  94 "
        pdb=" CB  ILE R  94 "
      ideal   model   delta    sigma   weight residual
     110.57  112.94   -2.37 1.28e+00 6.10e-01 3.42e+00
  angle pdb=" CB  MET R 279 "
        pdb=" CG  MET R 279 "
        pdb=" SD  MET R 279 "
      ideal   model   delta    sigma   weight residual
     112.70  117.41   -4.71 3.00e+00 1.11e-01 2.46e+00
  angle pdb=" C   SER R 207 "
        pdb=" N   PHE R 208 "
        pdb=" CA  PHE R 208 "
      ideal   model   delta    sigma   weight residual
     122.46  119.69    2.77 1.80e+00 3.09e-01 2.37e+00
  ... (remaining 3008 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.06: 1129
       17.06 -    34.12: 105
       34.12 -    51.18: 20
       51.18 -    68.24: 0
       68.24 -    85.30: 3
  Dihedral angle restraints: 1257
    sinusoidal: 429
      harmonic: 828
  Sorted by residual:
  dihedral pdb=" CB  CYS R 106 "
           pdb=" SG  CYS R 106 "
           pdb=" SG  CYS R 191 "
           pdb=" CB  CYS R 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -171.30   85.30     1      1.00e+01 1.00e-02 8.81e+01
  dihedral pdb=" CA  TYR R 174 "
           pdb=" C   TYR R 174 "
           pdb=" N   ARG R 175 "
           pdb=" CA  ARG R 175 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.22  -17.78     0      5.00e+00 4.00e-02 1.26e+01
  dihedral pdb=" CA  PHE R 208 "
           pdb=" C   PHE R 208 "
           pdb=" N   TYR R 209 "
           pdb=" CA  TYR R 209 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.84  -16.16     0      5.00e+00 4.00e-02 1.04e+01
  ... (remaining 1254 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 218
       0.029 -    0.058: 102
       0.058 -    0.087: 36
       0.087 -    0.116: 14
       0.116 -    0.145: 2
  Chirality restraints: 372
  Sorted by residual:
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.54   -0.14 2.00e-01 2.50e+01 5.22e-01
  chirality pdb=" CA  PRO R 138 "
            pdb=" N   PRO R 138 "
            pdb=" C   PRO R 138 "
            pdb=" CB  PRO R 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.48e-01
  chirality pdb=" CA  PRO R 288 "
            pdb=" N   PRO R 288 "
            pdb=" C   PRO R 288 "
            pdb=" CB  PRO R 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 2.98e-01
  ... (remaining 369 not shown)

  Planarity restraints: 359
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 167 "   -0.025 5.00e-02 4.00e+02   3.81e-02 2.32e+00
        pdb=" N   PRO R 168 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO R 168 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO R 168 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 173 "   -0.010 2.00e-02 2.50e+03   6.01e-03 9.03e-01
        pdb=" CG  TRP R 173 "    0.016 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 173 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 173 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 173 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 173 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 173 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 173 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 173 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 173 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR R 174 "   -0.005 2.00e-02 2.50e+03   6.69e-03 8.96e-01
        pdb=" CG  TYR R 174 "    0.016 2.00e-02 2.50e+03
        pdb=" CD1 TYR R 174 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR R 174 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR R 174 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR R 174 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR R 174 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR R 174 "    0.001 2.00e-02 2.50e+03
  ... (remaining 356 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 822
        2.89 -     3.39: 2198
        3.39 -     3.89: 3321
        3.89 -     4.40: 3453
        4.40 -     4.90: 6239
  Nonbonded interactions: 16033
  Sorted by model distance:
  nonbonded pdb=" OH  TYR R 185 "
            pdb=" O   PHE R 194 "
     model   vdw
     2.387 3.040
  nonbonded pdb=" OD1 ASN R 196 "
            pdb=" N   GLN R 197 "
     model   vdw
     2.475 3.120
  nonbonded pdb=" OG  SER R 120 "
            pdb=" O   HOH R 601 "
     model   vdw
     2.519 3.040
  nonbonded pdb=" OE1 GLU R 107 "
            pdb=" OH  TYR R 174 "
     model   vdw
     2.524 3.040
  nonbonded pdb=" O   THR R 189 "
            pdb=" OG1 THR R 189 "
     model   vdw
     2.525 3.040
  ... (remaining 16028 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             2.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.880
  Find NCS groups from input model:        0.010
  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:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
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   0.053   2199  Z= 0.191
  Angle     :  0.543   5.602   3015  Z= 0.287
  Chirality :  0.040   0.145    372
  Planarity :  0.004   0.038    359
  Dihedral  : 13.102  72.445    716
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  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 are not related in a simple way.
  whole:  1.94 (0.51), residues: 277
  helix:  2.21 (0.35), residues: 212
  sheet:  None (None), residues: 0
  loop : -2.00 (0.65), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 175 
 TYR   0.016   0.001   TYR R 174 
 PHE   0.014   0.001   PHE R 139 
 TRP   0.016   0.001   TRP R 173 
 HIS   0.003   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 2198)
  covalent geometry    : angle       0.54315 ( 3013)
  SS BOND              : bond        0.00232 (    1)
  SS BOND              : angle       0.42313 (    2)
  hydrogen bonds       : bond        0.13862 (  163)
  hydrogen bonds       : angle       5.24854 (  486)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.1021
  time to fit residues: 3.2446
Evaluate side-chains
  24 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0070
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0010
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.3804

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

Flipped N/Q/H residues before XYZ refinement:
R 296 HIS
R 312 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.132888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.118627 restraints weight = 3021.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 1.75
r_work: 0.3250 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3148 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.0900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   2199  Z= 0.121
  Angle     :  0.455   5.053   3015  Z= 0.250
  Chirality :  0.038   0.116    372
  Planarity :  0.003   0.031    359
  Dihedral  :  4.107  16.718    310
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 2.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  :  6.48 %
    Favored  : 89.81 %
  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 are not related in a simple way.
  whole:  2.43 (0.52), residues: 277
  helix:  2.37 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.76 (0.79), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 175 
 TYR   0.006   0.001   TYR R 308 
 PHE   0.009   0.001   PHE R 282 
 TRP   0.005   0.001   TRP R 173 
 HIS   0.003   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 2198)
  covalent geometry    : angle       0.45476 ( 3013)
  SS BOND              : bond        0.00146 (    1)
  SS BOND              : angle       0.17678 (    2)
  hydrogen bonds       : bond        0.05696 (  163)
  hydrogen bonds       : angle       4.04828 (  486)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 24
  time to evaluate  : 0.077 
Fit side-chains
REVERT: R  334 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8091 (mp)
  outliers start: 8
  outliers final: 4
  residues processed: 31
  average time/residue: 0.0820
  time to fit residues: 2.9373
Evaluate side-chains
  27 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  182 ILE
Chi-restraints excluded: chain R residue  334 ILE
Chi-restraints excluded: chain R residue  340 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 26 optimal weight:    0.0270
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.6238

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

Flipped N/Q/H residues before XYZ refinement:
R 178 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.129060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.115024 restraints weight = 3168.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 1.75
r_work: 0.3198 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3096 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.1053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2199  Z= 0.143
  Angle     :  0.482   5.157   3015  Z= 0.267
  Chirality :  0.039   0.111    372
  Planarity :  0.003   0.027    359
  Dihedral  :  4.181  16.673    310
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 13.89 %
    Favored  : 83.33 %
  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 are not related in a simple way.
  whole:  2.39 (0.51), residues: 277
  helix:  2.37 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.86 (0.79), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG R 175 
 TYR   0.006   0.001   TYR R 308 
 PHE   0.012   0.001   PHE R 282 
 TRP   0.004   0.001   TRP R 109 
 HIS   0.005   0.002   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 2198)
  covalent geometry    : angle       0.48185 ( 3013)
  SS BOND              : bond        0.00236 (    1)
  SS BOND              : angle       0.21608 (    2)
  hydrogen bonds       : bond        0.06336 (  163)
  hydrogen bonds       : angle       3.96743 (  486)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 21
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
REVERT: R  334 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8121 (mp)
  outliers start: 6
  outliers final: 4
  residues processed: 26
  average time/residue: 0.0967
  time to fit residues: 2.8654
Evaluate side-chains
  26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  334 ILE
Chi-restraints excluded: chain R residue  340 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0470
   chunk 8 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
R 312 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.129644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.114925 restraints weight = 3145.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 1.91
r_work: 0.3193 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.1142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   2199  Z= 0.131
  Angle     :  0.461   5.117   3015  Z= 0.255
  Chirality :  0.038   0.111    372
  Planarity :  0.003   0.027    359
  Dihedral  :  4.169  16.718    310
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.20 %
    Favored  : 81.48 %
  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 are not related in a simple way.
  whole:  2.47 (0.51), residues: 277
  helix:  2.44 (0.34), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.93 (0.78), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG R 175 
 TYR   0.007   0.001   TYR R 308 
 PHE   0.010   0.001   PHE R 282 
 TRP   0.004   0.001   TRP R 173 
 HIS   0.003   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 2198)
  covalent geometry    : angle       0.46069 ( 3013)
  SS BOND              : bond        0.00186 (    1)
  SS BOND              : angle       0.19753 (    2)
  hydrogen bonds       : bond        0.06049 (  163)
  hydrogen bonds       : angle       3.90353 (  486)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 20
  time to evaluate  : 0.074 
Fit side-chains
   revert: symmetry clash
REVERT: R  334 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8083 (mp)
  outliers start: 5
  outliers final: 3
  residues processed: 25
  average time/residue: 0.0998
  time to fit residues: 2.8364
Evaluate side-chains
  24 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 20
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  334 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0980
   chunk 15 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3432 r_free = 0.3432 target = 0.128105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.114127 restraints weight = 3113.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.72
r_work: 0.3186 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.1246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2199  Z= 0.138
  Angle     :  0.470   5.137   3015  Z= 0.259
  Chirality :  0.039   0.110    372
  Planarity :  0.003   0.027    359
  Dihedral  :  4.157  16.690    310
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 17.13 %
    Favored  : 80.56 %
  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 are not related in a simple way.
  whole:  2.48 (0.51), residues: 277
  helix:  2.44 (0.34), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.92 (0.78), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG R 175 
 TYR   0.007   0.001   TYR R 308 
 PHE   0.010   0.001   PHE R 282 
 TRP   0.004   0.001   TRP R  99 
 HIS   0.003   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 2198)
  covalent geometry    : angle       0.47005 ( 3013)
  SS BOND              : bond        0.00197 (    1)
  SS BOND              : angle       0.21913 (    2)
  hydrogen bonds       : bond        0.06203 (  163)
  hydrogen bonds       : angle       3.89686 (  486)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.078 
Fit side-chains
   revert: symmetry clash
REVERT: R   72 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7763 (mp)
REVERT: R  334 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8087 (mp)
  outliers start: 5
  outliers final: 3
  residues processed: 27
  average time/residue: 0.0940
  time to fit residues: 2.9019
Evaluate side-chains
  26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  334 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 13 optimal weight:    0.1980
   chunk 19 optimal weight:    0.8980
   chunk 10 optimal weight:    0.3980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3441 r_free = 0.3441 target = 0.128644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.114568 restraints weight = 3096.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 1.70
r_work: 0.3194 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3092 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2199  Z= 0.130
  Angle     :  0.458   5.116   3015  Z= 0.252
  Chirality :  0.038   0.110    372
  Planarity :  0.003   0.026    359
  Dihedral  :  4.137  16.691    310
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 16.67 %
    Favored  : 80.56 %
  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 are not related in a simple way.
  whole:  2.52 (0.51), residues: 277
  helix:  2.46 (0.34), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.87 (0.80), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 175 
 TYR   0.007   0.001   TYR R 308 
 PHE   0.010   0.001   PHE R 282 
 TRP   0.004   0.001   TRP R 173 
 HIS   0.002   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 2198)
  covalent geometry    : angle       0.45764 ( 3013)
  SS BOND              : bond        0.00158 (    1)
  SS BOND              : angle       0.22897 (    2)
  hydrogen bonds       : bond        0.05962 (  163)
  hydrogen bonds       : angle       3.85163 (  486)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
REVERT: R   72 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7776 (mp)
REVERT: R  334 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.8071 (mp)
  outliers start: 6
  outliers final: 3
  residues processed: 28
  average time/residue: 0.0902
  time to fit residues: 2.8844
Evaluate side-chains
  27 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  334 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 15 optimal weight:    0.1980
   chunk 21 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
R 312 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.127636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.113506 restraints weight = 3104.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 1.72
r_work: 0.3181 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.1360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2199  Z= 0.136
  Angle     :  0.466   5.126   3015  Z= 0.257
  Chirality :  0.039   0.109    372
  Planarity :  0.003   0.026    359
  Dihedral  :  4.188  16.661    310
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 18.06 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.49 (0.52), residues: 277
  helix:  2.45 (0.34), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.89 (0.81), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 175 
 TYR   0.007   0.001   TYR R 308 
 PHE   0.011   0.001   PHE R 282 
 TRP   0.004   0.001   TRP R  99 
 HIS   0.002   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 2198)
  covalent geometry    : angle       0.46579 ( 3013)
  SS BOND              : bond        0.00185 (    1)
  SS BOND              : angle       0.24457 (    2)
  hydrogen bonds       : bond        0.06180 (  163)
  hydrogen bonds       : angle       3.88060 (  486)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
REVERT: R   72 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7821 (mp)
REVERT: R  334 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8094 (mp)
  outliers start: 5
  outliers final: 3
  residues processed: 27
  average time/residue: 0.0950
  time to fit residues: 2.9263
Evaluate side-chains
  26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  334 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 10 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 24 optimal weight:    0.4980
   chunk 27 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
R 312 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.126442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.112438 restraints weight = 3116.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 1.71
r_work: 0.3163 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3064 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2199  Z= 0.150
  Angle     :  0.477   5.159   3015  Z= 0.265
  Chirality :  0.039   0.110    372
  Planarity :  0.003   0.027    359
  Dihedral  :  4.234  16.699    310
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 18.06 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.39 (0.52), residues: 277
  helix:  2.36 (0.34), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.87 (0.82), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 175 
 TYR   0.011   0.001   TYR R 185 
 PHE   0.011   0.001   PHE R 282 
 TRP   0.004   0.001   TRP R  99 
 HIS   0.003   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 2198)
  covalent geometry    : angle       0.47722 ( 3013)
  SS BOND              : bond        0.00227 (    1)
  SS BOND              : angle       0.24516 (    2)
  hydrogen bonds       : bond        0.06551 (  163)
  hydrogen bonds       : angle       3.94072 (  486)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 23
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
REVERT: R   72 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7824 (mp)
REVERT: R  334 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8124 (mp)
  outliers start: 5
  outliers final: 3
  residues processed: 28
  average time/residue: 0.0920
  time to fit residues: 2.9534
Evaluate side-chains
  28 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 23
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  334 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 24 optimal weight:    0.2980
   chunk 10 optimal weight:    0.5980
   chunk 26 optimal weight:    0.2980
   chunk 3 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3442 r_free = 0.3442 target = 0.128655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.113955 restraints weight = 3101.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.90
r_work: 0.3179 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3075 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.1423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2199  Z= 0.127
  Angle     :  0.454   5.093   3015  Z= 0.253
  Chirality :  0.038   0.108    372
  Planarity :  0.003   0.027    359
  Dihedral  :  4.118  16.875    310
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 1.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.59 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.52 (0.52), residues: 277
  helix:  2.44 (0.34), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.74 (0.84), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 175 
 TYR   0.007   0.001   TYR R 185 
 PHE   0.010   0.001   PHE R 282 
 TRP   0.005   0.001   TRP R 173 
 HIS   0.002   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 2198)
  covalent geometry    : angle       0.45457 ( 3013)
  SS BOND              : bond        0.00131 (    1)
  SS BOND              : angle       0.22338 (    2)
  hydrogen bonds       : bond        0.05943 (  163)
  hydrogen bonds       : angle       3.82857 (  486)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.046 
Fit side-chains
   revert: symmetry clash
REVERT: R   72 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7824 (mp)
REVERT: R  334 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8090 (mp)
  outliers start: 6
  outliers final: 3
  residues processed: 28
  average time/residue: 0.0855
  time to fit residues: 2.7313
Evaluate side-chains
  28 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 23
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  334 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 14 optimal weight:    0.0000
   chunk 22 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0570
   chunk 20 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.4502

-------------------------------------------------------------------------------
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 = 0.3450 r_free = 0.3450 target = 0.129188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.114999 restraints weight = 3097.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 1.73
r_work: 0.3202 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   2199  Z= 0.122
  Angle     :  0.448   5.092   3015  Z= 0.249
  Chirality :  0.038   0.106    372
  Planarity :  0.003   0.027    359
  Dihedral  :  4.076  16.810    310
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 18.52 %
    Favored  : 79.17 %
  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 are not related in a simple way.
  whole:  2.59 (0.52), residues: 277
  helix:  2.49 (0.34), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.74 (0.83), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 175 
 TYR   0.007   0.001   TYR R 185 
 PHE   0.010   0.001   PHE R 282 
 TRP   0.005   0.001   TRP R 173 
 HIS   0.002   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 2198)
  covalent geometry    : angle       0.44784 ( 3013)
  SS BOND              : bond        0.00092 (    1)
  SS BOND              : angle       0.21118 (    2)
  hydrogen bonds       : bond        0.05679 (  163)
  hydrogen bonds       : angle       3.78269 (  486)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 23
  time to evaluate  : 0.075 
Fit side-chains
   revert: symmetry clash
REVERT: R   72 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7783 (mp)
REVERT: R  334 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8074 (mp)
  outliers start: 5
  outliers final: 3
  residues processed: 28
  average time/residue: 0.0900
  time to fit residues: 2.8876
Evaluate side-chains
  28 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 23
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  334 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0270
   chunk 7 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.5638

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.128488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.114313 restraints weight = 3158.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 1.74
r_work: 0.3192 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2199  Z= 0.134
  Angle     :  0.491   8.316   3015  Z= 0.264
  Chirality :  0.038   0.107    372
  Planarity :  0.003   0.027    359
  Dihedral  :  4.111  16.677    310
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 18.98 %
    Favored  : 78.70 %
  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 are not related in a simple way.
  whole:  2.51 (0.52), residues: 277
  helix:  2.43 (0.34), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.77 (0.84), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 175 
 TYR   0.007   0.001   TYR R 308 
 PHE   0.010   0.001   PHE R 282 
 TRP   0.005   0.001   TRP R 173 
 HIS   0.002   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 2198)
  covalent geometry    : angle       0.49160 ( 3013)
  SS BOND              : bond        0.00148 (    1)
  SS BOND              : angle       0.22768 (    2)
  hydrogen bonds       : bond        0.05984 (  163)
  hydrogen bonds       : angle       3.83819 (  486)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 808.28 seconds
wall clock time: 14 minutes 53.27 seconds (893.27 seconds total)