Starting phenix.real_space_refine
on Tue Feb  3 15:24:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9az3_44008/02_2026/9az3_44008.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9az3_44008/02_2026/9az3_44008.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9az3_44008/02_2026/9az3_44008.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9az3_44008/02_2026/9az3_44008.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9az3_44008/02_2026/9az3_44008.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9az3_44008/02_2026/9az3_44008.map"
  }
  resolution = 3.9
  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=   0.002
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      38      5.16       5
     C    2646      2.51       5
     N     726      2.21       5
     O     793      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s

  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: 4203
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "G"
      Number of atoms: 2021
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 2021
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 12, 'TRANS': 244}
          Chain breaks: 1
    Chain: "N"
      Number of atoms: 2084
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 260, 2084
          Classifications: {'peptide': 260}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 243}
          Chain breaks: 3
    Chain: "G"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "N"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 0.94, per 1000 atoms: 0.22
  Number of scatterers: 4203
  At special positions: 0
  Unit cell: (82.944, 97.2, 104.976, 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      38     16.00
     O     793      8.00
     N     726      7.00
     C    2646      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=13, symmetry=0
    Simple disulfide: pdb=" SG  CYS G  69 " - pdb=" SG  CYS G  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  77 " - pdb=" SG  CYS G  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 182 " - pdb=" SG  CYS G 205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 286 " - pdb=" SG  CYS G 295 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G 288 " - pdb=" SG  CYS G 305 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  53 " - pdb=" SG  CYS N  80 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  62 " - pdb=" SG  CYS N  77 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  72 " - pdb=" SG  CYS N 236 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 164 " - pdb=" SG  CYS N 181 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N 191 " - pdb=" SG  CYS N 234 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 262 " - pdb=" SG  CYS N 271 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 264 " - pdb=" SG  CYS N 293 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 295 " - pdb=" SG  CYS N 304 " 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: 0.21
  Conformation dependent library (CDL) restraints added in 97.6 milliseconds
  

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  980

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 7 sheets defined
      11.6% alpha, 11.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'G' and resid 102 through 107
      removed outlier: 3.715A  pdb=" N   LEU G 106 " --> pdb=" O   GLY G 102 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 122 through 126
    Processing helix  chain 'G' and resid 181 through 186
      removed outlier: 3.652A  pdb=" N   THR G 185 " --> pdb=" O   SER G 181 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 233 through 236
    Processing helix  chain 'G' and resid 237 through 245
    Processing helix  chain 'G' and resid 266 through 273
      removed outlier: 3.529A  pdb=" N   LYS G 271 " --> pdb=" O   PRO G 267 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 90 through 94
    Processing helix  chain 'N' and resid 163 through 168
    Processing helix  chain 'N' and resid 202 through 206
      removed outlier: 3.583A  pdb=" N   ASP N 206 " --> pdb=" O   PRO N 203 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 212 through 217
      removed outlier: 3.803A  pdb=" N   GLU N 217 " --> pdb=" O   ALA N 213 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'G' and resid 55 through 56
    Processing sheet with id=AA2, first strand: chain 'G' and resid 55 through 56
      removed outlier: 4.116A  pdb=" N   TYR G 147 " --> pdb=" O   GLY G 283 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'G' and resid 63 through 64
      removed outlier: 3.962A  pdb=" N   LEU G 135 " --> pdb=" O   VAL G 251 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ASP G 248 " --> pdb=" O   ARG G 165 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   PHE G 160 " --> pdb=" O   TYR G 177 " (cutoff:3.500A)
      removed outlier: 5.801A  pdb=" N   TYR G 177 " --> pdb=" O   PHE G 160 " (cutoff:3.500A)
      removed outlier: 7.672A  pdb=" N   ILE G 162 " --> pdb=" O   TYR G 175 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   TYR G 175 " --> pdb=" O   ILE G 162 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'G' and resid 76 through 77
    Processing sheet with id=AA5, first strand: chain 'N' and resid 125 through 126
    Processing sheet with id=AA6, first strand: chain 'N' and resid 142 through 146
      removed outlier: 3.712A  pdb=" N   VAL N 143 " --> pdb=" O   ARG N 227 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   ARG N 227 " --> pdb=" O   VAL N 143 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   ASP N 145 " --> pdb=" O   ARG N 225 " (cutoff:3.500A)
      removed outlier: 4.701A  pdb=" N   ARG N 225 " --> pdb=" O   ASP N 145 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'N' and resid 299 through 300
      removed outlier: 4.220A  pdb=" N   HIS N 306 " --> pdb=" O   ALA N 300 " (cutoff:3.500A)

    50 hydrogen bonds defined for protein.
    108 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: 0.37

  Time building geometry restraints manager: 0.30 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1327
        1.34 -     1.46: 1071
        1.46 -     1.59: 1873
        1.59 -     1.71: 0
        1.71 -     1.84: 47
  Bond restraints: 4318
  Sorted by residual:
  bond pdb=" N   CYS G 305 "
       pdb=" CA  CYS G 305 "
    ideal  model  delta    sigma   weight residual
    1.454  1.503 -0.049 1.21e-02 6.83e+03 1.62e+01
  bond pdb=" N   LEU G 303 "
       pdb=" CA  LEU G 303 "
    ideal  model  delta    sigma   weight residual
    1.460  1.500 -0.041 1.20e-02 6.94e+03 1.14e+01
  bond pdb=" N   VAL G 304 "
       pdb=" CA  VAL G 304 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.11e-02 8.12e+03 1.05e+01
  bond pdb=" N   CYS G 288 "
       pdb=" CA  CYS G 288 "
    ideal  model  delta    sigma   weight residual
    1.458  1.500 -0.042 1.44e-02 4.82e+03 8.69e+00
  bond pdb=" N   ASN G 306 "
       pdb=" CA  ASN G 306 "
    ideal  model  delta    sigma   weight residual
    1.453  1.491 -0.038 1.31e-02 5.83e+03 8.42e+00
  ... (remaining 4313 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 5712
        2.33 -     4.65: 126
        4.65 -     6.98: 16
        6.98 -     9.30: 3
        9.30 -    11.63: 2
  Bond angle restraints: 5859
  Sorted by residual:
  angle pdb=" N   HIS G 291 "
        pdb=" CA  HIS G 291 "
        pdb=" C   HIS G 291 "
      ideal   model   delta    sigma   weight residual
     112.87  101.24   11.63 1.20e+00 6.94e-01 9.39e+01
  angle pdb=" N   ASN G 289 "
        pdb=" CA  ASN G 289 "
        pdb=" C   ASN G 289 "
      ideal   model   delta    sigma   weight residual
     112.24  103.57    8.67 1.28e+00 6.10e-01 4.58e+01
  angle pdb=" N   MET G 296 "
        pdb=" CA  MET G 296 "
        pdb=" C   MET G 296 "
      ideal   model   delta    sigma   weight residual
     109.25   99.37    9.88 1.53e+00 4.27e-01 4.17e+01
  angle pdb=" CA  VAL G 304 "
        pdb=" C   VAL G 304 "
        pdb=" O   VAL G 304 "
      ideal   model   delta    sigma   weight residual
     121.67  115.13    6.54 1.05e+00 9.07e-01 3.87e+01
  angle pdb=" CA  ASN G 306 "
        pdb=" C   ASN G 306 "
        pdb=" O   ASN G 306 "
      ideal   model   delta    sigma   weight residual
     121.94  114.95    6.99 1.15e+00 7.56e-01 3.69e+01
  ... (remaining 5854 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 2359
       17.58 -    35.16: 228
       35.16 -    52.74: 62
       52.74 -    70.32: 19
       70.32 -    87.90: 6
  Dihedral angle restraints: 2674
    sinusoidal: 1159
      harmonic: 1515
  Sorted by residual:
  dihedral pdb=" CB  CYS G  69 "
           pdb=" SG  CYS G  69 "
           pdb=" SG  CYS G  92 "
           pdb=" CB  CYS G  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -157.92   71.92     1      1.00e+01 1.00e-02 6.62e+01
  dihedral pdb=" CB  CYS G 286 "
           pdb=" SG  CYS G 286 "
           pdb=" SG  CYS G 295 "
           pdb=" CB  CYS G 295 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -149.46   63.46     1      1.00e+01 1.00e-02 5.31e+01
  dihedral pdb=" CB  CYS N 164 "
           pdb=" SG  CYS N 164 "
           pdb=" SG  CYS N 181 "
           pdb=" CB  CYS N 181 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -32.09  -53.91     1      1.00e+01 1.00e-02 3.95e+01
  ... (remaining 2671 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 524
       0.050 -    0.101: 79
       0.101 -    0.151: 23
       0.151 -    0.202: 3
       0.202 -    0.252: 2
  Chirality restraints: 631
  Sorted by residual:
  chirality pdb=" CA  ARG G 285 "
            pdb=" N   ARG G 285 "
            pdb=" C   ARG G 285 "
            pdb=" CB  ARG G 285 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CA  ILE G 145 "
            pdb=" N   ILE G 145 "
            pdb=" C   ILE G 145 "
            pdb=" CB  ILE G 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CA  ASP G 144 "
            pdb=" N   ASP G 144 "
            pdb=" C   ASP G 144 "
            pdb=" CB  ASP G 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.25e-01
  ... (remaining 628 not shown)

  Planarity restraints: 753
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER G 293 "    0.031 2.00e-02 2.50e+03   6.06e-02 3.67e+01
        pdb=" C   SER G 293 "   -0.105 2.00e-02 2.50e+03
        pdb=" O   SER G 293 "    0.039 2.00e-02 2.50e+03
        pdb=" N   GLU G 294 "    0.035 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU G 139 "   -0.023 2.00e-02 2.50e+03   4.52e-02 2.04e+01
        pdb=" C   LEU G 139 "    0.078 2.00e-02 2.50e+03
        pdb=" O   LEU G 139 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   GLY G 140 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG G 285 "   -0.015 2.00e-02 2.50e+03   3.12e-02 9.71e+00
        pdb=" C   ARG G 285 "    0.054 2.00e-02 2.50e+03
        pdb=" O   ARG G 285 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   CYS G 286 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 750 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 123
        2.62 -     3.19: 4191
        3.19 -     3.76: 6216
        3.76 -     4.33: 8450
        4.33 -     4.90: 13187
  Nonbonded interactions: 32167
  Sorted by model distance:
  nonbonded pdb=" O   LYS G 308 "
            pdb=" OG1 THR G 311 "
     model   vdw
     2.055 3.040
  nonbonded pdb=" OG  SER G 230 "
            pdb=" OD1 ASN G 233 "
     model   vdw
     2.067 3.040
  nonbonded pdb=" O   GLN N  74 "
            pdb=" NZ  LYS N  76 "
     model   vdw
     2.095 3.120
  nonbonded pdb=" O   VAL G  61 "
            pdb=" OG1 THR G 107 "
     model   vdw
     2.098 3.040
  nonbonded pdb=" OD1 ASN N 163 "
            pdb=" OG  SER N 165 "
     model   vdw
     2.099 3.040
  ... (remaining 32162 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.580
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.580
  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:0.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5697
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   0.049   4331  Z= 0.258
  Angle     :  0.823  11.626   5885  Z= 0.514
  Chirality :  0.045   0.252    631
  Planarity :  0.005   0.061    753
  Dihedral  : 15.268  87.899   1655
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.49 %
    Favored  : 88.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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 (0.36), residues: 505
  helix: -1.46 (1.16), residues: 19
  sheet: -3.53 (0.78), residues: 37
  loop : -1.43 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG N 225 
 TYR   0.016   0.001   TYR G 175 
 PHE   0.014   0.001   PHE N 134 
 TRP   0.010   0.001   TRP G 243 
 HIS   0.007   0.001   HIS G 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 4318)
  covalent geometry    : angle       0.82005 ( 5859)
  SS BOND              : bond        0.00468 (   13)
  SS BOND              : angle       1.33481 (   26)
  hydrogen bonds       : bond        0.34849 (   48)
  hydrogen bonds       : angle      15.90996 (  108)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.099 
Fit side-chains
REVERT: N  250 HIS cc_start: 0.7770 (p-80) cc_final: 0.7471 (p-80)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.0291
  time to fit residues: 2.2277
Evaluate side-chains
  44 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:   10.0000
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0010
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
G 119 GLN
N  86 HIS
** N 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 148 GLN
N 287 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.162660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.150204 restraints weight = 15306.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.152898 restraints weight = 9531.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.154767 restraints weight = 6515.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.156055 restraints weight = 4751.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.156984 restraints weight = 3663.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.4461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5702
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4331  Z= 0.126
  Angle     :  0.654   9.109   5885  Z= 0.330
  Chirality :  0.044   0.228    631
  Planarity :  0.005   0.040    753
  Dihedral  :  7.461  59.693    706
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.90 %
    Favored  : 90.10 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 10.29 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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: -2.44 (0.35), residues: 505
  helix: -2.05 (0.72), residues: 36
  sheet: -2.92 (0.76), residues: 42
  loop : -1.58 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N 146 
 TYR   0.017   0.002   TYR G 175 
 PHE   0.014   0.001   PHE N 134 
 TRP   0.014   0.001   TRP N 154 
 HIS   0.002   0.001   HIS G 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 4318)
  covalent geometry    : angle       0.65135 ( 5859)
  SS BOND              : bond        0.00270 (   13)
  SS BOND              : angle       1.13923 (   26)
  hydrogen bonds       : bond        0.04979 (   48)
  hydrogen bonds       : angle      11.65657 (  108)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.166 
Fit side-chains
REVERT: G  169 ASP cc_start: 0.7234 (t0) cc_final: 0.6958 (t0)
  outliers start: 7
  outliers final: 4
  residues processed: 51
  average time/residue: 0.0509
  time to fit residues: 3.6727
Evaluate side-chains
  45 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  295 CYS
Chi-restraints excluded: chain N residue   70 LEU
Chi-restraints excluded: chain N residue   71 THR
Chi-restraints excluded: chain N residue  196 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0170
   chunk 42 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   chunk 31 optimal weight:    6.9990
   chunk 27 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.1422

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

Flipped N/Q/H residues before XYZ refinement:
G  60 ASN
** N 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.171019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.160823 restraints weight = 18344.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4558 r_free = 0.4558 target = 0.163031 restraints weight = 11376.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.164093 restraints weight = 7251.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.164835 restraints weight = 5122.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.165030 restraints weight = 4555.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.4420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5781
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4331  Z= 0.151
  Angle     :  0.670   9.628   5885  Z= 0.335
  Chirality :  0.044   0.252    631
  Planarity :  0.005   0.039    753
  Dihedral  :  7.257  58.175    706
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.69 %
    Favored  : 89.31 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 16.55 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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: -2.58 (0.34), residues: 505
  helix: -2.23 (0.69), residues: 36
  sheet: -3.03 (0.73), residues: 39
  loop : -1.69 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG N  73 
 TYR   0.020   0.002   TYR G 175 
 PHE   0.017   0.002   PHE G 280 
 TRP   0.014   0.002   TRP N 154 
 HIS   0.004   0.001   HIS G 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 4318)
  covalent geometry    : angle       0.66758 ( 5859)
  SS BOND              : bond        0.00307 (   13)
  SS BOND              : angle       1.13679 (   26)
  hydrogen bonds       : bond        0.04096 (   48)
  hydrogen bonds       : angle      11.01613 (  108)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.162 
Fit side-chains
REVERT: G  169 ASP cc_start: 0.7413 (t0) cc_final: 0.7000 (t0)
REVERT: N  250 HIS cc_start: 0.7645 (p-80) cc_final: 0.7227 (p-80)
  outliers start: 9
  outliers final: 6
  residues processed: 55
  average time/residue: 0.0398
  time to fit residues: 3.3594
Evaluate side-chains
  48 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  143 PHE
Chi-restraints excluded: chain G residue  295 CYS
Chi-restraints excluded: chain N residue   70 LEU
Chi-restraints excluded: chain N residue   71 THR
Chi-restraints excluded: chain N residue  196 VAL
Chi-restraints excluded: chain N residue  323 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 27 optimal weight:    0.2980
   chunk 24 optimal weight:    0.0770
   chunk 18 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 48 optimal weight:   10.0000
   chunk 15 optimal weight:    0.0470
   chunk 17 optimal weight:    0.0970
   overall best weight:    0.2834

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

Flipped N/Q/H residues before XYZ refinement:
** N 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.162640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.150308 restraints weight = 15849.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.152850 restraints weight = 10198.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.154610 restraints weight = 7150.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.155915 restraints weight = 5324.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.156839 restraints weight = 4140.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.4467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5691
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   4331  Z= 0.104
  Angle     :  0.616   9.576   5885  Z= 0.305
  Chirality :  0.042   0.244    631
  Planarity :  0.004   0.040    753
  Dihedral  :  6.539  55.909    706
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.31 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 18.34 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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: -2.41 (0.35), residues: 505
  helix: -2.25 (0.71), residues: 36
  sheet: -2.28 (0.70), residues: 49
  loop : -1.59 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG N 146 
 TYR   0.011   0.001   TYR N 157 
 PHE   0.012   0.001   PHE G 280 
 TRP   0.009   0.001   TRP N 154 
 HIS   0.003   0.001   HIS N 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 4318)
  covalent geometry    : angle       0.61286 ( 5859)
  SS BOND              : bond        0.00229 (   13)
  SS BOND              : angle       1.05805 (   26)
  hydrogen bonds       : bond        0.03221 (   48)
  hydrogen bonds       : angle       9.83964 (  108)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.158 
Fit side-chains
REVERT: G  169 ASP cc_start: 0.7334 (t0) cc_final: 0.6823 (t0)
REVERT: N   61 PHE cc_start: 0.7486 (p90) cc_final: 0.7278 (p90)
REVERT: N   94 MET cc_start: 0.1782 (mtp) cc_final: 0.1416 (mmt)
REVERT: N  250 HIS cc_start: 0.7571 (p-80) cc_final: 0.7179 (p-80)
  outliers start: 9
  outliers final: 6
  residues processed: 54
  average time/residue: 0.0445
  time to fit residues: 3.5227
Evaluate side-chains
  51 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   71 THR
Chi-restraints excluded: chain G residue   85 VAL
Chi-restraints excluded: chain G residue  282 VAL
Chi-restraints excluded: chain N residue   70 LEU
Chi-restraints excluded: chain N residue   71 THR
Chi-restraints excluded: chain N residue  196 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 2 optimal weight:    0.0980
   chunk 28 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** N 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4634 r_free = 0.4634 target = 0.164869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.156115 restraints weight = 17578.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.157865 restraints weight = 11299.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.159093 restraints weight = 7932.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.159939 restraints weight = 5930.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4557 r_free = 0.4557 target = 0.160526 restraints weight = 4675.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.4427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5768
moved from start:          0.2882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4331  Z= 0.129
  Angle     :  0.648   9.611   5885  Z= 0.322
  Chirality :  0.042   0.249    631
  Planarity :  0.004   0.039    753
  Dihedral  :  6.657  55.948    706
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.50 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 19.46 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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: -2.53 (0.35), residues: 505
  helix: -2.19 (0.73), residues: 36
  sheet: -2.28 (0.69), residues: 49
  loop : -1.71 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N 103 
 TYR   0.011   0.001   TYR N 157 
 PHE   0.017   0.002   PHE G 280 
 TRP   0.009   0.001   TRP N 154 
 HIS   0.003   0.001   HIS G 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 4318)
  covalent geometry    : angle       0.64590 ( 5859)
  SS BOND              : bond        0.00312 (   13)
  SS BOND              : angle       1.08223 (   26)
  hydrogen bonds       : bond        0.03429 (   48)
  hydrogen bonds       : angle       9.66739 (  108)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 0.092 
Fit side-chains
REVERT: G  169 ASP cc_start: 0.7441 (t0) cc_final: 0.7016 (t0)
REVERT: G  209 PHE cc_start: 0.5255 (OUTLIER) cc_final: 0.4453 (p90)
REVERT: G  294 GLU cc_start: 0.3877 (OUTLIER) cc_final: 0.3078 (tp30)
REVERT: N  250 HIS cc_start: 0.7705 (p-80) cc_final: 0.7321 (p-80)
  outliers start: 14
  outliers final: 9
  residues processed: 58
  average time/residue: 0.0274
  time to fit residues: 2.4232
Evaluate side-chains
  56 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   71 THR
Chi-restraints excluded: chain G residue   85 VAL
Chi-restraints excluded: chain G residue  209 PHE
Chi-restraints excluded: chain G residue  212 ILE
Chi-restraints excluded: chain G residue  216 THR
Chi-restraints excluded: chain G residue  282 VAL
Chi-restraints excluded: chain G residue  294 GLU
Chi-restraints excluded: chain N residue   70 LEU
Chi-restraints excluded: chain N residue   71 THR
Chi-restraints excluded: chain N residue  196 VAL
Chi-restraints excluded: chain N residue  323 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 7 optimal weight:    0.5980
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
G 291 HIS
** N 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4636 r_free = 0.4636 target = 0.172201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.162216 restraints weight = 18887.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4578 r_free = 0.4578 target = 0.164510 restraints weight = 11730.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.165697 restraints weight = 7238.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4608 r_free = 0.4608 target = 0.166494 restraints weight = 4935.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4611 r_free = 0.4611 target = 0.166668 restraints weight = 4233.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.4443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5726
moved from start:          0.3103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4331  Z= 0.122
  Angle     :  0.632   9.608   5885  Z= 0.314
  Chirality :  0.042   0.248    631
  Planarity :  0.004   0.039    753
  Dihedral  :  6.473  56.000    706
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.10 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 19.91 %
    Favored  : 76.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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: -2.58 (0.35), residues: 505
  helix: -2.30 (0.72), residues: 36
  sheet: -2.02 (0.71), residues: 47
  loop : -1.78 (0.29), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N 103 
 TYR   0.016   0.001   TYR G 129 
 PHE   0.016   0.001   PHE G 280 
 TRP   0.010   0.001   TRP N 154 
 HIS   0.003   0.001   HIS G 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4318)
  covalent geometry    : angle       0.63039 ( 5859)
  SS BOND              : bond        0.00402 (   13)
  SS BOND              : angle       0.95670 (   26)
  hydrogen bonds       : bond        0.03133 (   48)
  hydrogen bonds       : angle       9.24553 (  108)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 52
  time to evaluate  : 0.165 
Fit side-chains
REVERT: G  169 ASP cc_start: 0.7435 (t0) cc_final: 0.7052 (t0)
REVERT: G  175 TYR cc_start: 0.5985 (OUTLIER) cc_final: 0.5439 (m-10)
REVERT: G  209 PHE cc_start: 0.5367 (OUTLIER) cc_final: 0.4697 (p90)
REVERT: G  241 GLN cc_start: 0.7164 (mm-40) cc_final: 0.6943 (mm-40)
REVERT: G  291 HIS cc_start: 0.5420 (OUTLIER) cc_final: 0.4870 (t70)
REVERT: N   61 PHE cc_start: 0.7536 (p90) cc_final: 0.7264 (p90)
REVERT: N  250 HIS cc_start: 0.7665 (p-80) cc_final: 0.7264 (p-80)
  outliers start: 17
  outliers final: 12
  residues processed: 64
  average time/residue: 0.0376
  time to fit residues: 3.5535
Evaluate side-chains
  66 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   71 THR
Chi-restraints excluded: chain G residue   85 VAL
Chi-restraints excluded: chain G residue  143 PHE
Chi-restraints excluded: chain G residue  175 TYR
Chi-restraints excluded: chain G residue  205 CYS
Chi-restraints excluded: chain G residue  209 PHE
Chi-restraints excluded: chain G residue  216 THR
Chi-restraints excluded: chain G residue  282 VAL
Chi-restraints excluded: chain G residue  291 HIS
Chi-restraints excluded: chain N residue   70 LEU
Chi-restraints excluded: chain N residue   71 THR
Chi-restraints excluded: chain N residue  196 VAL
Chi-restraints excluded: chain N residue  234 CYS
Chi-restraints excluded: chain N residue  271 CYS
Chi-restraints excluded: chain N residue  323 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0010
   chunk 31 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 1 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 44 optimal weight:    6.9990
   chunk 6 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.8788

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

Flipped N/Q/H residues before XYZ refinement:
** G 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4630 r_free = 0.4630 target = 0.171786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4562 r_free = 0.4562 target = 0.161809 restraints weight = 18798.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.164068 restraints weight = 11545.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.165156 restraints weight = 7339.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.165749 restraints weight = 5067.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.166007 restraints weight = 4562.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.4435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5753
moved from start:          0.3225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4331  Z= 0.130
  Angle     :  0.674   9.626   5885  Z= 0.333
  Chirality :  0.042   0.250    631
  Planarity :  0.004   0.039    753
  Dihedral  :  6.495  56.007    706
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.70 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 21.25 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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: -2.73 (0.35), residues: 505
  helix: -2.31 (0.74), residues: 36
  sheet: -2.95 (0.73), residues: 37
  loop : -1.84 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N 103 
 TYR   0.012   0.001   TYR N 157 
 PHE   0.017   0.002   PHE G 280 
 TRP   0.010   0.001   TRP N 154 
 HIS   0.004   0.001   HIS G 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 4318)
  covalent geometry    : angle       0.67125 ( 5859)
  SS BOND              : bond        0.00488 (   13)
  SS BOND              : angle       1.18358 (   26)
  hydrogen bonds       : bond        0.03294 (   48)
  hydrogen bonds       : angle       9.18473 (  108)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 0.176 
Fit side-chains
REVERT: G  169 ASP cc_start: 0.7470 (t0) cc_final: 0.7072 (t0)
REVERT: G  175 TYR cc_start: 0.6196 (OUTLIER) cc_final: 0.5483 (m-10)
REVERT: G  209 PHE cc_start: 0.5377 (OUTLIER) cc_final: 0.4680 (p90)
REVERT: G  216 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8328 (m)
REVERT: N   61 PHE cc_start: 0.7591 (p90) cc_final: 0.7282 (p90)
  outliers start: 12
  outliers final: 9
  residues processed: 60
  average time/residue: 0.0494
  time to fit residues: 4.3628
Evaluate side-chains
  60 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   71 THR
Chi-restraints excluded: chain G residue   85 VAL
Chi-restraints excluded: chain G residue  175 TYR
Chi-restraints excluded: chain G residue  205 CYS
Chi-restraints excluded: chain G residue  209 PHE
Chi-restraints excluded: chain G residue  216 THR
Chi-restraints excluded: chain G residue  282 VAL
Chi-restraints excluded: chain N residue   71 THR
Chi-restraints excluded: chain N residue  196 VAL
Chi-restraints excluded: chain N residue  215 VAL
Chi-restraints excluded: chain N residue  271 CYS
Chi-restraints excluded: chain N residue  323 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 10 optimal weight:    0.4980
   chunk 32 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** G 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.155764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.143024 restraints weight = 16569.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.145536 restraints weight = 10812.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.147349 restraints weight = 7657.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.148639 restraints weight = 5747.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.149565 restraints weight = 4529.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.4372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5906
moved from start:          0.3430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4331  Z= 0.156
  Angle     :  0.696   9.652   5885  Z= 0.343
  Chirality :  0.043   0.255    631
  Planarity :  0.005   0.039    753
  Dihedral  :  6.801  56.132    706
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 14.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.88 %
    Favored  : 88.12 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 21.48 %
    Favored  : 74.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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: -2.87 (0.35), residues: 505
  helix: -2.33 (0.76), residues: 36
  sheet: -4.06 (0.72), residues: 27
  loop : -1.91 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG N  73 
 TYR   0.015   0.002   TYR G 129 
 PHE   0.019   0.002   PHE G 280 
 TRP   0.013   0.002   TRP N 154 
 HIS   0.007   0.001   HIS G 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 4318)
  covalent geometry    : angle       0.69426 ( 5859)
  SS BOND              : bond        0.00312 (   13)
  SS BOND              : angle       1.07790 (   26)
  hydrogen bonds       : bond        0.03631 (   48)
  hydrogen bonds       : angle       9.24564 (  108)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 54
  time to evaluate  : 0.087 
Fit side-chains
REVERT: G  169 ASP cc_start: 0.7426 (t0) cc_final: 0.7135 (t0)
REVERT: G  175 TYR cc_start: 0.6273 (OUTLIER) cc_final: 0.5638 (m-10)
REVERT: G  209 PHE cc_start: 0.5327 (OUTLIER) cc_final: 0.4579 (p90)
REVERT: N   61 PHE cc_start: 0.7641 (p90) cc_final: 0.7310 (p90)
REVERT: N  177 LYS cc_start: 0.5617 (tptt) cc_final: 0.5393 (mmmt)
REVERT: N  250 HIS cc_start: 0.7713 (p-80) cc_final: 0.7376 (p-80)
REVERT: N  256 PHE cc_start: 0.7612 (m-80) cc_final: 0.6940 (m-10)
  outliers start: 16
  outliers final: 12
  residues processed: 65
  average time/residue: 0.0339
  time to fit residues: 3.1155
Evaluate side-chains
  65 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   71 THR
Chi-restraints excluded: chain G residue   85 VAL
Chi-restraints excluded: chain G residue  143 PHE
Chi-restraints excluded: chain G residue  175 TYR
Chi-restraints excluded: chain G residue  205 CYS
Chi-restraints excluded: chain G residue  209 PHE
Chi-restraints excluded: chain G residue  282 VAL
Chi-restraints excluded: chain N residue   70 LEU
Chi-restraints excluded: chain N residue   71 THR
Chi-restraints excluded: chain N residue  196 VAL
Chi-restraints excluded: chain N residue  215 VAL
Chi-restraints excluded: chain N residue  234 CYS
Chi-restraints excluded: chain N residue  271 CYS
Chi-restraints excluded: chain N residue  323 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0870
   chunk 13 optimal weight:    0.0370
   chunk 23 optimal weight:    0.5980
   chunk 44 optimal weight:    0.2980
   chunk 26 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0870
   overall best weight:    0.2214

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

Flipped N/Q/H residues before XYZ refinement:
G 291 HIS
** N 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.162359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.149054 restraints weight = 16063.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.151673 restraints weight = 10500.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.153523 restraints weight = 7494.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.154790 restraints weight = 5667.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.155767 restraints weight = 4532.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.4458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5727
moved from start:          0.3557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   4331  Z= 0.112
  Angle     :  0.698  10.173   5885  Z= 0.340
  Chirality :  0.042   0.242    631
  Planarity :  0.004   0.039    753
  Dihedral  :  6.115  55.910    706
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.30 %
    Favored  : 89.70 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 22.37 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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: -2.66 (0.36), residues: 505
  helix: -2.31 (0.76), residues: 35
  sheet: -2.96 (0.76), residues: 37
  loop : -1.77 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 156 
 TYR   0.032   0.001   TYR N 157 
 PHE   0.016   0.001   PHE G 280 
 TRP   0.008   0.001   TRP N 154 
 HIS   0.003   0.000   HIS N 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 4318)
  covalent geometry    : angle       0.69449 ( 5859)
  SS BOND              : bond        0.00601 (   13)
  SS BOND              : angle       1.19667 (   26)
  hydrogen bonds       : bond        0.02808 (   48)
  hydrogen bonds       : angle       8.64035 (  108)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
REVERT: G  169 ASP cc_start: 0.7345 (t0) cc_final: 0.6997 (t0)
REVERT: G  175 TYR cc_start: 0.5867 (OUTLIER) cc_final: 0.5205 (m-10)
REVERT: G  209 PHE cc_start: 0.5298 (OUTLIER) cc_final: 0.4629 (p90)
REVERT: G  291 HIS cc_start: 0.5862 (OUTLIER) cc_final: 0.5556 (t70)
REVERT: N   61 PHE cc_start: 0.7495 (p90) cc_final: 0.7127 (p90)
REVERT: N   94 MET cc_start: 0.1359 (mtp) cc_final: -0.1066 (mmt)
REVERT: N  250 HIS cc_start: 0.7626 (p-80) cc_final: 0.7267 (p-80)
  outliers start: 11
  outliers final: 6
  residues processed: 62
  average time/residue: 0.0423
  time to fit residues: 3.8121
Evaluate side-chains
  61 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   71 THR
Chi-restraints excluded: chain G residue   85 VAL
Chi-restraints excluded: chain G residue  175 TYR
Chi-restraints excluded: chain G residue  209 PHE
Chi-restraints excluded: chain G residue  282 VAL
Chi-restraints excluded: chain G residue  291 HIS
Chi-restraints excluded: chain N residue   70 LEU
Chi-restraints excluded: chain N residue   71 THR
Chi-restraints excluded: chain N residue  215 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 43 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 15 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0570
   chunk 11 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:    0.4980
   chunk 21 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
G 291 HIS
** N 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.160081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.147691 restraints weight = 16030.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.150207 restraints weight = 10386.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.151975 restraints weight = 7326.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.153209 restraints weight = 5484.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.154071 restraints weight = 4320.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.4439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5775
moved from start:          0.3599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4331  Z= 0.116
  Angle     :  0.672   9.911   5885  Z= 0.327
  Chirality :  0.042   0.246    631
  Planarity :  0.004   0.039    753
  Dihedral  :  6.004  55.948    706
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.90 %
    Favored  : 90.10 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 23.04 %
    Favored  : 74.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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: -2.72 (0.36), residues: 505
  helix: -2.37 (0.76), residues: 35
  sheet: -2.69 (0.79), residues: 35
  loop : -1.86 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N 103 
 TYR   0.034   0.001   TYR N 157 
 PHE   0.015   0.001   PHE G 280 
 TRP   0.007   0.001   TRP N 154 
 HIS   0.003   0.001   HIS G 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 4318)
  covalent geometry    : angle       0.66917 ( 5859)
  SS BOND              : bond        0.00254 (   13)
  SS BOND              : angle       1.10978 (   26)
  hydrogen bonds       : bond        0.03024 (   48)
  hydrogen bonds       : angle       8.73559 (  108)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.162 
Fit side-chains
REVERT: G  169 ASP cc_start: 0.7248 (t0) cc_final: 0.6891 (t0)
REVERT: G  175 TYR cc_start: 0.6031 (OUTLIER) cc_final: 0.5278 (m-10)
REVERT: G  209 PHE cc_start: 0.5256 (OUTLIER) cc_final: 0.4616 (p90)
REVERT: N   61 PHE cc_start: 0.7512 (p90) cc_final: 0.7149 (p90)
REVERT: N  250 HIS cc_start: 0.7730 (p-80) cc_final: 0.7419 (p-80)
REVERT: N  256 PHE cc_start: 0.7340 (m-80) cc_final: 0.6743 (m-10)
  outliers start: 10
  outliers final: 7
  residues processed: 59
  average time/residue: 0.0466
  time to fit residues: 3.9793
Evaluate side-chains
  61 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   71 THR
Chi-restraints excluded: chain G residue   85 VAL
Chi-restraints excluded: chain G residue  175 TYR
Chi-restraints excluded: chain G residue  209 PHE
Chi-restraints excluded: chain G residue  282 VAL
Chi-restraints excluded: chain G residue  291 HIS
Chi-restraints excluded: chain N residue   70 LEU
Chi-restraints excluded: chain N residue   71 THR
Chi-restraints excluded: chain N residue  215 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0770
   chunk 24 optimal weight:    0.0470
   chunk 35 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   chunk 2 optimal weight:    0.4980
   chunk 44 optimal weight:    5.9990
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.3836

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

Flipped N/Q/H residues before XYZ refinement:
G 291 HIS
** N 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.161622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.149603 restraints weight = 16915.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.153374 restraints weight = 11649.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.154026 restraints weight = 7413.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.155173 restraints weight = 6413.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.156257 restraints weight = 4927.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.4472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5700
moved from start:          0.3673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4331  Z= 0.108
  Angle     :  0.683   9.585   5885  Z= 0.331
  Chirality :  0.042   0.244    631
  Planarity :  0.004   0.039    753
  Dihedral  :  5.902  55.897    706
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.90 %
    Favored  : 90.10 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 23.27 %
    Favored  : 74.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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: -2.66 (0.36), residues: 505
  helix: -2.50 (0.73), residues: 35
  sheet: -2.15 (0.69), residues: 49
  loop : -1.82 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 285 
 TYR   0.033   0.001   TYR N 157 
 PHE   0.015   0.001   PHE G 280 
 TRP   0.007   0.001   TRP N 154 
 HIS   0.004   0.001   HIS G 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 4318)
  covalent geometry    : angle       0.68104 ( 5859)
  SS BOND              : bond        0.00418 (   13)
  SS BOND              : angle       1.00963 (   26)
  hydrogen bonds       : bond        0.02856 (   48)
  hydrogen bonds       : angle       8.54372 (  108)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 742.96 seconds
wall clock time: 13 minutes 32.46 seconds (812.46 seconds total)