Starting phenix.real_space_refine
on Fri Aug 22 12:37:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gh1_40028/08_2025/8gh1_40028.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gh1_40028/08_2025/8gh1_40028.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gh1_40028/08_2025/8gh1_40028.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gh1_40028/08_2025/8gh1_40028.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gh1_40028/08_2025/8gh1_40028.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gh1_40028/08_2025/8gh1_40028.cif"
  }
  resolution = 4.1
  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=   0.015
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      10      5.16       5
     C    1299      2.51       5
     N     328      2.21       5
     O     339      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 1976
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 1961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 1961
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 95}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 303
          Unresolved non-hydrogen angles: 385
          Unresolved non-hydrogen dihedrals: 234
          Unresolved non-hydrogen chiralities: 46
          Planarities with less than four sites: {'TRP:plan': 1, 'ASN:plan1': 6, 'ARG:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 8, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 122
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.57, per 1000 atoms: 0.29
  Number of scatterers: 1976
  At special positions: 0
  Unit cell: (55.5328, 86.77, 65.0775, 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      10     16.00
     O     339      8.00
     N     328      7.00
     C    1299      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 184 " - pdb=" SG  CYS R 190 " 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: 0.11
  Conformation dependent library (CDL) restraints added in 81.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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:
      11 helices and 0 sheets defined
      85.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.03
  Creating SS restraints...
    Processing helix  chain 'R' and resid 31 through 60
      removed outlier: 3.557A  pdb=" N   GLY R  35 " --> pdb=" O   VAL R  31 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   VAL R  48 " --> pdb=" O   VAL R  44 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   PHE R  49 " --> pdb=" O   LEU R  45 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LEU R  53 " --> pdb=" O   PHE R  49 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   VAL R  54 " --> pdb=" O   GLY R  50 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 96
      removed outlier: 3.686A  pdb=" N   TYR R  70 " --> pdb=" O   THR R  66 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 4.241A  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 105 through 137
      removed outlier: 3.602A  pdb=" N   SER R 137 " --> pdb=" O   PHE R 133 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 3.949A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   SER R 143 " --> pdb=" O   PHE R 139 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LEU R 145 " --> pdb=" O   TYR R 141 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.662A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ILE R 153 " --> pdb=" O   LYS R 149 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ILE R 154 " --> pdb=" O   ALA R 150 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
      removed outlier: 3.516A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 181 through 187
    Processing helix  chain 'R' and resid 196 through 208
      removed outlier: 3.575A  pdb=" N   ALA R 200 " --> pdb=" O   ASN R 196 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ILE R 201 " --> pdb=" O   GLN R 197 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 236
      removed outlier: 4.037A  pdb=" N   SER R 236 " --> pdb=" O   LYS R 232 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 296
      removed outlier: 3.973A  pdb=" N   THR R 274 " --> pdb=" O   LYS R 270 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ILE R 278 " --> pdb=" O   THR R 274 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   CYS R 285 " --> pdb=" O   THR R 281 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.710A  pdb=" N   VAL R 295 " --> pdb=" O   ILE R 291 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   HIS R 296 " --> pdb=" O   VAL R 292 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 327
      removed outlier: 3.682A  pdb=" N   GLY R 315 " --> pdb=" O   LEU R 311 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   TYR R 316 " --> pdb=" O   ASN R 312 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 340
      removed outlier: 3.523A  pdb=" N   LEU R 339 " --> pdb=" O   ALA R 335 " (cutoff:3.500A)

    153 hydrogen bonds defined for protein.
    459 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: 0.19

  Time building geometry restraints manager: 0.14 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 621
        1.34 -     1.46: 529
        1.46 -     1.58: 867
        1.58 -     1.69: 0
        1.69 -     1.81: 13
  Bond restraints: 2030
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.452 -0.055 2.00e-02 2.50e+03 7.45e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.443 -0.049 2.00e-02 2.50e+03 6.00e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.570 -0.047 2.00e-02 2.50e+03 5.48e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.567 -0.047 2.00e-02 2.50e+03 5.43e+00
  bond pdb=" CAE G1I R 501 "
       pdb=" CAG G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.506  1.539 -0.033 2.00e-02 2.50e+03 2.66e+00
  ... (remaining 2025 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.12: 2664
        1.12 -     2.23: 105
        2.23 -     3.35: 11
        3.35 -     4.47: 5
        4.47 -     5.58: 9
  Bond angle restraints: 2794
  Sorted by residual:
  angle pdb=" C   GLU R 107 "
        pdb=" N   PHE R 108 "
        pdb=" CA  PHE R 108 "
      ideal   model   delta    sigma   weight residual
     121.58  116.26    5.32 1.95e+00 2.63e-01 7.44e+00
  angle pdb=" N   TYR R 326 "
        pdb=" CA  TYR R 326 "
        pdb=" C   TYR R 326 "
      ideal   model   delta    sigma   weight residual
     111.36  114.23   -2.87 1.09e+00 8.42e-01 6.92e+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  117.66   -5.03 3.00e+00 1.11e-01 2.81e+00
  angle pdb=" CA  LEU R 230 "
        pdb=" CB  LEU R 230 "
        pdb=" CG  LEU R 230 "
      ideal   model   delta    sigma   weight residual
     116.30  121.88   -5.58 3.50e+00 8.16e-02 2.54e+00
  angle pdb=" CAG G1I R 501 "
        pdb=" CAH G1I R 501 "
        pdb=" CAI G1I R 501 "
      ideal   model   delta    sigma   weight residual
     110.89  115.56   -4.67 3.00e+00 1.11e-01 2.42e+00
  ... (remaining 2789 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.96: 1028
       14.96 -    29.91: 93
       29.91 -    44.87: 19
       44.87 -    59.82: 3
       59.82 -    74.78: 3
  Dihedral angle restraints: 1146
    sinusoidal: 318
      harmonic: 828
  Sorted by residual:
  dihedral pdb=" CB  CYS R 184 "
           pdb=" SG  CYS R 184 "
           pdb=" SG  CYS R 190 "
           pdb=" CB  CYS R 190 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  167.78  -74.78     1      1.00e+01 1.00e-02 7.08e+01
  dihedral pdb=" CA  ILE R 277 "
           pdb=" C   ILE R 277 "
           pdb=" N   ILE R 278 "
           pdb=" CA  ILE R 278 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.43  -17.57     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  ASP R 234 "
           pdb=" CB  ASP R 234 "
           pdb=" CG  ASP R 234 "
           pdb=" OD1 ASP R 234 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.10   55.10     1      2.00e+01 2.50e-03 1.03e+01
  ... (remaining 1143 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 213
       0.035 -    0.070: 99
       0.070 -    0.105: 17
       0.105 -    0.140: 1
       0.140 -    0.174: 1
  Chirality restraints: 331
  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    2.57   -0.17 2.00e-01 2.50e+01 7.61e-01
  chirality pdb=" CA  PHE R 108 "
            pdb=" N   PHE R 108 "
            pdb=" C   PHE R 108 "
            pdb=" CB  PHE R 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.39e-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    0.10 2.00e-01 2.50e+01 2.74e-01
  ... (remaining 328 not shown)

  Planarity restraints: 351
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 283 "    0.004 2.00e-02 2.50e+03   8.55e-03 7.32e-01
        pdb=" C   THR R 283 "   -0.015 2.00e-02 2.50e+03
        pdb=" O   THR R 283 "    0.006 2.00e-02 2.50e+03
        pdb=" N   LEU R 284 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER R 137 "    0.014 5.00e-02 4.00e+02   2.13e-02 7.24e-01
        pdb=" N   PRO R 138 "   -0.037 5.00e-02 4.00e+02
        pdb=" CA  PRO R 138 "    0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO R 138 "    0.012 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP R 109 "    0.004 2.00e-02 2.50e+03   8.40e-03 7.05e-01
        pdb=" C   TRP R 109 "   -0.015 2.00e-02 2.50e+03
        pdb=" O   TRP R 109 "    0.005 2.00e-02 2.50e+03
        pdb=" N   THR R 110 "    0.005 2.00e-02 2.50e+03
  ... (remaining 348 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 451
        2.78 -     3.31: 2008
        3.31 -     3.84: 3205
        3.84 -     4.37: 2963
        4.37 -     4.90: 5438
  Nonbonded interactions: 14065
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP R 113 "
            pdb=" OAM G1I R 501 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   SER R 236 "
            pdb=" OG  SER R 236 "
     model   vdw
     2.508 3.040
  nonbonded pdb=" OD2 ASP R 113 "
            pdb=" OH  TYR R 316 "
     model   vdw
     2.522 3.040
  nonbonded pdb=" O   GLU R 107 "
            pdb=" OG1 THR R 110 "
     model   vdw
     2.524 3.040
  nonbonded pdb=" O   TYR R  70 "
            pdb=" OG1 THR R  73 "
     model   vdw
     2.541 3.040
  ... (remaining 14060 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.650
  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:          0.030
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     2.800
  Find NCS groups from input model:        0.000
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
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   0.055   2031  Z= 0.184
  Angle     :  0.570   5.584   2796  Z= 0.294
  Chirality :  0.040   0.174    331
  Planarity :  0.003   0.025    351
  Dihedral  : 12.639  70.305    605
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.62 (0.52), residues: 277
  helix:  1.88 (0.38), residues: 204
  sheet:  None (None), residues: 0
  loop : -1.28 (0.71), residues: 73

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG R 131 
 TYR   0.005   0.001   TYR R 308 
 PHE   0.011   0.001   PHE R 108 
 TRP   0.013   0.001   TRP R 158 
 HIS   0.003   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 2030)
  covalent geometry    : angle       0.57008 ( 2794)
  SS BOND              : bond        0.00131 (    1)
  SS BOND              : angle       0.42931 (    2)
  hydrogen bonds       : bond        0.17032 (  153)
  hydrogen bonds       : angle       5.08112 (  459)

*********************** 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
  42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.050 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.0369
  time to fit residues: 1.8121
Evaluate side-chains
  32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.041 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0870
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0370
   chunk 9 optimal weight:    0.0470
   overall best weight:    0.3936

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.142359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.127836 restraints weight = 4341.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.130593 restraints weight = 2424.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.132459 restraints weight = 1569.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.133752 restraints weight = 1115.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.134684 restraints weight = 857.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.1166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2031  Z= 0.126
  Angle     :  0.528   5.125   2796  Z= 0.285
  Chirality :  0.039   0.131    331
  Planarity :  0.004   0.025    351
  Dihedral  :  4.790  14.928    310
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.96 (0.52), residues: 277
  helix:  1.97 (0.37), residues: 207
  sheet:  None (None), residues: 0
  loop : -0.74 (0.71), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 131 
 TYR   0.007   0.001   TYR R 326 
 PHE   0.023   0.002   PHE R 332 
 TRP   0.009   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 2030)
  covalent geometry    : angle       0.52840 ( 2794)
  SS BOND              : bond        0.00122 (    1)
  SS BOND              : angle       0.38024 (    2)
  hydrogen bonds       : bond        0.05353 (  153)
  hydrogen bonds       : angle       3.53380 (  459)

*********************** 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
  52 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.043 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.0266
  time to fit residues: 1.7525
Evaluate side-chains
  32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 5 optimal weight:    0.4980
   chunk 23 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0050
   chunk 10 optimal weight:    0.0980
   chunk 9 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 1 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0470
   overall best weight:    0.2492

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.144814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.129619 restraints weight = 4476.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.132556 restraints weight = 2487.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.134597 restraints weight = 1602.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.136068 restraints weight = 1128.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.137024 restraints weight = 855.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   2031  Z= 0.105
  Angle     :  0.465   5.055   2796  Z= 0.253
  Chirality :  0.038   0.121    331
  Planarity :  0.003   0.027    351
  Dihedral  :  4.359  14.907    310
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 2.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.19 (0.52), residues: 277
  helix:  2.34 (0.38), residues: 198
  sheet:  None (None), residues: 0
  loop : -0.95 (0.67), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG R 131 
 TYR   0.006   0.001   TYR R 308 
 PHE   0.015   0.001   PHE R 108 
 TRP   0.008   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00193 ( 2030)
  covalent geometry    : angle       0.46547 ( 2794)
  SS BOND              : bond        0.00203 (    1)
  SS BOND              : angle       0.34021 (    2)
  hydrogen bonds       : bond        0.04383 (  153)
  hydrogen bonds       : angle       3.21227 (  459)

*********************** 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
  51 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.043 
Fit side-chains
REVERT: R  174 TYR cc_start: 0.8145 (p90) cc_final: 0.7769 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.0351
  time to fit residues: 2.1277
Evaluate side-chains
  33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0020
   chunk 19 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0980
   chunk 17 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.4988

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.142722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.128755 restraints weight = 4307.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.131405 restraints weight = 2420.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.133205 restraints weight = 1573.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.134440 restraints weight = 1124.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.135425 restraints weight = 869.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2031  Z= 0.118
  Angle     :  0.502   5.297   2796  Z= 0.267
  Chirality :  0.037   0.114    331
  Planarity :  0.003   0.027    351
  Dihedral  :  4.283  14.701    310
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 1.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.15 (0.51), residues: 277
  helix:  2.37 (0.37), residues: 198
  sheet:  None (None), residues: 0
  loop : -1.14 (0.65), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 131 
 TYR   0.005   0.001   TYR R 308 
 PHE   0.029   0.002   PHE R 332 
 TRP   0.009   0.001   TRP R 109 
 HIS   0.002   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 2030)
  covalent geometry    : angle       0.50243 ( 2794)
  SS BOND              : bond        0.00179 (    1)
  SS BOND              : angle       0.22885 (    2)
  hydrogen bonds       : bond        0.04366 (  153)
  hydrogen bonds       : angle       3.24136 (  459)

*********************** 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
  46 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.078 
Fit side-chains
REVERT: R  174 TYR cc_start: 0.8176 (p90) cc_final: 0.7775 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.0442
  time to fit residues: 2.4996
Evaluate side-chains
  32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0020
   chunk 10 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 19 optimal weight:    0.2980
   chunk 14 optimal weight:    0.0030
   chunk 18 optimal weight:    0.1980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.2198

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.147069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.133524 restraints weight = 4482.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.136204 restraints weight = 2544.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.138031 restraints weight = 1653.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.139311 restraints weight = 1168.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.140125 restraints weight = 895.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   2031  Z= 0.099
  Angle     :  0.478   5.994   2796  Z= 0.248
  Chirality :  0.037   0.111    331
  Planarity :  0.003   0.025    351
  Dihedral  :  3.936  14.201    310
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.29 (0.52), residues: 277
  helix:  2.48 (0.37), residues: 198
  sheet:  None (None), residues: 0
  loop : -1.08 (0.67), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 131 
 TYR   0.005   0.001   TYR R 308 
 PHE   0.015   0.001   PHE R 108 
 TRP   0.009   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00183 ( 2030)
  covalent geometry    : angle       0.47773 ( 2794)
  SS BOND              : bond        0.00133 (    1)
  SS BOND              : angle       0.14705 (    2)
  hydrogen bonds       : bond        0.03812 (  153)
  hydrogen bonds       : angle       3.08338 (  459)

*********************** 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
  61 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.075 
Fit side-chains
REVERT: R   82 MET cc_start: 0.8813 (tmm) cc_final: 0.8576 (tmm)
REVERT: R  174 TYR cc_start: 0.8180 (p90) cc_final: 0.7774 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0456
  time to fit residues: 3.3614
Evaluate side-chains
  33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 11 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0870
   chunk 2 optimal weight:    0.3980
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.5358

-------------------------------------------------------------------------------
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 = 0.3732 r_free = 0.3732 target = 0.142463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.128542 restraints weight = 4381.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.131304 restraints weight = 2391.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.133155 restraints weight = 1515.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.134456 restraints weight = 1062.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.135401 restraints weight = 806.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2031  Z= 0.115
  Angle     :  0.505   5.250   2796  Z= 0.267
  Chirality :  0.037   0.108    331
  Planarity :  0.003   0.027    351
  Dihedral  :  4.048  14.221    310
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 2.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.28 (0.52), residues: 277
  helix:  2.48 (0.37), residues: 198
  sheet:  None (None), residues: 0
  loop : -1.10 (0.67), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 131 
 TYR   0.005   0.001   TYR R 199 
 PHE   0.030   0.002   PHE R 332 
 TRP   0.009   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 2030)
  covalent geometry    : angle       0.50513 ( 2794)
  SS BOND              : bond        0.00062 (    1)
  SS BOND              : angle       0.15451 (    2)
  hydrogen bonds       : bond        0.04286 (  153)
  hydrogen bonds       : angle       3.19891 (  459)

*********************** 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
  55 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.076 
Fit side-chains
REVERT: R   82 MET cc_start: 0.8882 (tmm) cc_final: 0.8607 (tmm)
REVERT: R  174 TYR cc_start: 0.8208 (p90) cc_final: 0.7911 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0427
  time to fit residues: 2.8925
Evaluate side-chains
  34 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3742 r_free = 0.3742 target = 0.141388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.126503 restraints weight = 4562.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.129206 restraints weight = 2557.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.131038 restraints weight = 1656.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.132372 restraints weight = 1177.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.133169 restraints weight = 907.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.2071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2031  Z= 0.133
  Angle     :  0.509   5.251   2796  Z= 0.276
  Chirality :  0.038   0.129    331
  Planarity :  0.003   0.028    351
  Dihedral  :  4.162  15.445    310
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 1.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.22 (0.51), residues: 277
  helix:  2.48 (0.37), residues: 197
  sheet:  None (None), residues: 0
  loop : -1.22 (0.67), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 131 
 TYR   0.006   0.001   TYR R 199 
 PHE   0.021   0.002   PHE R 108 
 TRP   0.012   0.001   TRP R 158 
 HIS   0.003   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 2030)
  covalent geometry    : angle       0.50902 ( 2794)
  SS BOND              : bond        0.00140 (    1)
  SS BOND              : angle       0.18049 (    2)
  hydrogen bonds       : bond        0.04788 (  153)
  hydrogen bonds       : angle       3.28973 (  459)

*********************** 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
  52 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.072 
Fit side-chains
REVERT: R   82 MET cc_start: 0.8899 (tmm) cc_final: 0.8619 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.0420
  time to fit residues: 2.6843
Evaluate side-chains
  33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0670
   chunk 9 optimal weight:    0.5980
   chunk 4 optimal weight:    4.9990
   chunk 24 optimal weight:    0.1980
   chunk 19 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 13 optimal weight:    0.4980
   overall best weight:    0.4318

-------------------------------------------------------------------------------
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 = 0.3748 r_free = 0.3748 target = 0.142929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.128969 restraints weight = 4617.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.131736 restraints weight = 2542.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.133628 restraints weight = 1614.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.134952 restraints weight = 1131.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.135848 restraints weight = 853.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2031  Z= 0.112
  Angle     :  0.507   5.256   2796  Z= 0.269
  Chirality :  0.038   0.122    331
  Planarity :  0.003   0.026    351
  Dihedral  :  4.071  14.389    310
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.27 (0.51), residues: 277
  helix:  2.48 (0.37), residues: 198
  sheet:  None (None), residues: 0
  loop : -1.14 (0.67), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG R 131 
 TYR   0.017   0.001   TYR R 174 
 PHE   0.032   0.002   PHE R 332 
 TRP   0.012   0.001   TRP R 158 
 HIS   0.003   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 2030)
  covalent geometry    : angle       0.50749 ( 2794)
  SS BOND              : bond        0.00117 (    1)
  SS BOND              : angle       0.14734 (    2)
  hydrogen bonds       : bond        0.04469 (  153)
  hydrogen bonds       : angle       3.26072 (  459)

*********************** 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
  49 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.078 
Fit side-chains
REVERT: R   82 MET cc_start: 0.8893 (tmm) cc_final: 0.8608 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.0452
  time to fit residues: 2.7128
Evaluate side-chains
  34 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   chunk 18 optimal weight:    0.0870
   chunk 20 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0370
   chunk 16 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0270
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.3094

-------------------------------------------------------------------------------
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 = 0.3794 r_free = 0.3794 target = 0.145632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.131746 restraints weight = 4535.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.134367 restraints weight = 2588.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.136248 restraints weight = 1688.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.137527 restraints weight = 1201.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.138364 restraints weight = 924.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   2031  Z= 0.102
  Angle     :  0.489   5.189   2796  Z= 0.258
  Chirality :  0.038   0.124    331
  Planarity :  0.003   0.025    351
  Dihedral  :  3.942  14.324    310
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.26 (0.52), residues: 277
  helix:  2.50 (0.37), residues: 199
  sheet:  None (None), residues: 0
  loop : -1.28 (0.66), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG R 131 
 TYR   0.007   0.001   TYR R 308 
 PHE   0.011   0.001   PHE R 108 
 TRP   0.012   0.001   TRP R 158 
 HIS   0.003   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00198 ( 2030)
  covalent geometry    : angle       0.48900 ( 2794)
  SS BOND              : bond        0.00110 (    1)
  SS BOND              : angle       0.16600 (    2)
  hydrogen bonds       : bond        0.04054 (  153)
  hydrogen bonds       : angle       3.19331 (  459)

*********************** 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
  49 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.075 
Fit side-chains
REVERT: R   82 MET cc_start: 0.8912 (tmm) cc_final: 0.8616 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.0494
  time to fit residues: 2.9104
Evaluate side-chains
  33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 7 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3735 r_free = 0.3735 target = 0.141026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.126964 restraints weight = 4726.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.129661 restraints weight = 2674.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.131432 restraints weight = 1729.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.132795 restraints weight = 1238.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.133673 restraints weight = 948.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2031  Z= 0.135
  Angle     :  0.527   5.593   2796  Z= 0.288
  Chirality :  0.039   0.116    331
  Planarity :  0.004   0.032    351
  Dihedral  :  4.225  17.053    310
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.16 (0.51), residues: 277
  helix:  2.32 (0.37), residues: 201
  sheet:  None (None), residues: 0
  loop : -1.09 (0.67), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 131 
 TYR   0.009   0.001   TYR R 219 
 PHE   0.017   0.002   PHE R 336 
 TRP   0.016   0.001   TRP R 158 
 HIS   0.005   0.002   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 2030)
  covalent geometry    : angle       0.52666 ( 2794)
  SS BOND              : bond        0.00145 (    1)
  SS BOND              : angle       0.24890 (    2)
  hydrogen bonds       : bond        0.04660 (  153)
  hydrogen bonds       : angle       3.35378 (  459)

********************** 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
  48 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.069 
Fit side-chains
REVERT: R   82 MET cc_start: 0.8901 (tmm) cc_final: 0.8603 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0433
  time to fit residues: 2.5484
Evaluate side-chains
  33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0970
   chunk 20 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.5578

-------------------------------------------------------------------------------
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 = 0.3743 r_free = 0.3743 target = 0.141549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.127568 restraints weight = 4801.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.130232 restraints weight = 2698.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.131961 restraints weight = 1739.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.133258 restraints weight = 1244.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.134216 restraints weight = 953.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   2031  Z= 0.118
  Angle     :  0.529   6.053   2796  Z= 0.282
  Chirality :  0.039   0.127    331
  Planarity :  0.003   0.030    351
  Dihedral  :  4.187  16.215    310
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.09 (0.51), residues: 277
  helix:  2.29 (0.37), residues: 201
  sheet:  None (None), residues: 0
  loop : -1.19 (0.66), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 131 
 TYR   0.007   0.001   TYR R 219 
 PHE   0.029   0.002   PHE R 332 
 TRP   0.018   0.001   TRP R 158 
 HIS   0.002   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 2030)
  covalent geometry    : angle       0.52895 ( 2794)
  SS BOND              : bond        0.00134 (    1)
  SS BOND              : angle       0.15793 (    2)
  hydrogen bonds       : bond        0.04599 (  153)
  hydrogen bonds       : angle       3.38412 (  459)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 620.53 seconds
wall clock time: 11 minutes 33.66 seconds (693.66 seconds total)