Starting phenix.real_space_refine
on Fri May  9 13:43:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggi_40009/05_2025/8ggi_40009.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggi_40009/05_2025/8ggi_40009.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ggi_40009/05_2025/8ggi_40009.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggi_40009/05_2025/8ggi_40009.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggi_40009/05_2025/8ggi_40009.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggi_40009/05_2025/8ggi_40009.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    1470      2.51       5
     N     348      2.21       5
     O     370      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 2203
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2186
          Classifications: {'peptide': 284}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 7, 'TRANS': 276}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 97
          Unresolved non-hydrogen angles: 121
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 67
    Chain: "R"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 17
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1, 'water': 2}
          Link IDs: {None: 2}
  Time building chain proxies: 2.41, per 1000 atoms: 1.09
  Number of scatterers: 2203
  At special positions: 0
  Unit cell: (54.6651, 83.2992, 63.3421, 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      15     16.00
     O     370      8.00
     N     348      7.00
     C    1470      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 184 " - pdb=" SG  CYS R 190 " distance=1.41

  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: 0.52
  Conformation dependent library (CDL) restraints added in 248.7 milliseconds
  

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  544

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 0 sheets defined
      82.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'R' and resid 29 through 61
      removed outlier: 3.553A  pdb=" N   VAL R  33 " --> pdb=" O   ASP R  29 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   VAL R  44 " --> pdb=" O   MET R  40 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU R  53 " --> pdb=" O   PHE R  49 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   VAL R  54 " --> pdb=" O   GLY R  50 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ILE R  55 " --> pdb=" O   ASN R  51 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 69 through 97
      removed outlier: 4.624A  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 103 through 136
      removed outlier: 4.114A  pdb=" N   GLU R 107 " --> pdb=" O   ASN R 103 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   PHE R 108 " --> pdb=" O   PHE R 104 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   TRP R 109 " --> pdb=" O   TRP R 105 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA R 134 " --> pdb=" O   ASP R 130 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ILE R 135 " --> pdb=" O   ARG R 131 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   THR R 136 " --> pdb=" O   TYR R 132 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 163
      removed outlier: 3.657A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 166 through 171
    Processing helix  chain 'R' and resid 178 through 186
    Processing helix  chain 'R' and resid 196 through 208
      removed outlier: 3.686A  pdb=" N   SER R 204 " --> pdb=" O   ALA R 200 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 238
      removed outlier: 3.953A  pdb=" N   ARG R 221 " --> pdb=" O   PHE R 217 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   VAL R 222 " --> pdb=" O   VAL R 218 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE R 223 " --> pdb=" O   TYR R 219 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   SER R 236 " --> pdb=" O   LYS R 232 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 280
    Processing helix  chain 'R' and resid 286 through 299
      removed outlier: 3.692A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 4.849A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.569A  pdb=" N   GLY R 315 " --> pdb=" O   LEU R 311 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 318 through 320
      No H-bonds generated for 'chain 'R' and resid 318 through 320'
    Processing helix  chain 'R' and resid 321 through 327
    Processing helix  chain 'R' and resid 329 through 340

    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: 0.52

  Time building geometry restraints manager: 0.61 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 651
        1.34 -     1.46: 581
        1.46 -     1.58: 1004
        1.58 -     1.70: 0
        1.70 -     1.83: 21
  Bond restraints: 2257
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.450 -0.053 2.00e-02 2.50e+03 6.97e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.439 -0.045 2.00e-02 2.50e+03 5.06e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.567 -0.044 2.00e-02 2.50e+03 4.87e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.563 -0.043 2.00e-02 2.50e+03 4.54e+00
  bond pdb=" C   CYS R 191 "
       pdb=" O   CYS R 191 "
    ideal  model  delta    sigma   weight residual
    1.235  1.220  0.015 7.50e-03 1.78e+04 4.18e+00
  ... (remaining 2252 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 3021
        1.88 -     3.75: 44
        3.75 -     5.63: 16
        5.63 -     7.51: 3
        7.51 -     9.38: 3
  Bond angle restraints: 3087
  Sorted by residual:
  angle pdb=" N   THR R 189 "
        pdb=" CA  THR R 189 "
        pdb=" C   THR R 189 "
      ideal   model   delta    sigma   weight residual
     114.04  104.66    9.38 1.24e+00 6.50e-01 5.73e+01
  angle pdb=" N   PHE R 193 "
        pdb=" CA  PHE R 193 "
        pdb=" C   PHE R 193 "
      ideal   model   delta    sigma   weight residual
     108.67  116.73   -8.06 1.55e+00 4.16e-01 2.70e+01
  angle pdb=" N   CYS R 191 "
        pdb=" CA  CYS R 191 "
        pdb=" C   CYS R 191 "
      ideal   model   delta    sigma   weight residual
     113.21  106.63    6.58 1.40e+00 5.10e-01 2.21e+01
  angle pdb=" N   CYS R 190 "
        pdb=" CA  CYS R 190 "
        pdb=" C   CYS R 190 "
      ideal   model   delta    sigma   weight residual
     109.96  115.88   -5.92 1.50e+00 4.44e-01 1.56e+01
  angle pdb=" N   CYS R 191 "
        pdb=" CA  CYS R 191 "
        pdb=" CB  CYS R 191 "
      ideal   model   delta    sigma   weight residual
     110.65  115.26   -4.61 1.71e+00 3.42e-01 7.28e+00
  ... (remaining 3082 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.08: 1151
       16.08 -    32.17: 122
       32.17 -    48.25: 25
       48.25 -    64.33: 3
       64.33 -    80.42: 3
  Dihedral angle restraints: 1304
    sinusoidal: 467
      harmonic: 837
  Sorted by residual:
  dihedral pdb=" CA  PHE R 208 "
           pdb=" C   PHE R 208 "
           pdb=" N   TYR R 209 "
           pdb=" CA  TYR R 209 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.92  -17.08     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  SER R 207 "
           pdb=" C   SER R 207 "
           pdb=" N   PHE R 208 "
           pdb=" CA  PHE R 208 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.16  -15.84     0      5.00e+00 4.00e-02 1.00e+01
  dihedral pdb=" CB  MET R 171 "
           pdb=" CG  MET R 171 "
           pdb=" SD  MET R 171 "
           pdb=" CE  MET R 171 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  117.75  -57.75     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 1301 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 232
       0.033 -    0.066: 102
       0.066 -    0.098: 33
       0.098 -    0.131: 10
       0.131 -    0.164: 1
  Chirality restraints: 378
  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    2.56   -0.16 2.00e-01 2.50e+01 6.70e-01
  chirality pdb=" CA  LEU R 287 "
            pdb=" N   LEU R 287 "
            pdb=" C   LEU R 287 "
            pdb=" CB  LEU R 287 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 3.02e-01
  chirality pdb=" CA  PRO R  88 "
            pdb=" N   PRO R  88 "
            pdb=" C   PRO R  88 "
            pdb=" CB  PRO R  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 2.96e-01
  ... (remaining 375 not shown)

  Planarity restraints: 368
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS R 190 "    0.012 2.00e-02 2.50e+03   2.47e-02 6.12e+00
        pdb=" C   CYS R 190 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   CYS R 190 "    0.016 2.00e-02 2.50e+03
        pdb=" N   CYS R 191 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU R 237 "    0.006 2.00e-02 2.50e+03   1.24e-02 1.54e+00
        pdb=" CD  GLU R 237 "   -0.021 2.00e-02 2.50e+03
        pdb=" OE1 GLU R 237 "    0.008 2.00e-02 2.50e+03
        pdb=" OE2 GLU R 237 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 313 "   -0.006 2.00e-02 2.50e+03   7.40e-03 1.37e+00
        pdb=" CG  TRP R 313 "    0.019 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 313 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 313 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 313 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 313 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 313 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 313 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 313 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 313 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 365 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 445
        2.77 -     3.31: 2101
        3.31 -     3.84: 3493
        3.84 -     4.37: 3684
        4.37 -     4.90: 6782
  Nonbonded interactions: 16505
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAL G1I R 501 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" N   GLU R 306 "
            pdb=" OE1 GLU R 306 "
     model   vdw
     2.333 3.120
  nonbonded pdb=" OH  TYR R 326 "
            pdb=" O   HOH R 601 "
     model   vdw
     2.407 3.040
  nonbonded pdb=" OH  TYR R 209 "
            pdb=" O   PHE R 290 "
     model   vdw
     2.450 3.040
  nonbonded pdb=" O   LEU R  64 "
            pdb=" ND2 ASN R  69 "
     model   vdw
     2.495 3.120
  ... (remaining 16500 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.800
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.520
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
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      :  0.014   0.622   2259  Z= 0.684
  Angle     :  0.805  18.619   3091  Z= 0.435
  Chirality :  0.042   0.164    378
  Planarity :  0.004   0.030    368
  Dihedral  : 13.755  80.416    754
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.51), residues: 280
  helix:  1.60 (0.37), residues: 204
  sheet:  None (None), residues: 0
  loop : -0.70 (0.71), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 313 
 HIS   0.005   0.002   HIS R 296 
 PHE   0.007   0.001   PHE R 193 
 TYR   0.007   0.001   TYR R 132 
 ARG   0.007   0.001   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16886 (  153)
  hydrogen bonds       : angle       5.56873 (  459)
  SS BOND              : bond        0.43999 (    2)
  SS BOND              : angle      11.40898 (    4)
  covalent geometry    : bond        0.00397 ( 2257)
  covalent geometry    : angle       0.69241 ( 3087)

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

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

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.247 
Fit side-chains
REVERT: R   82 MET cc_start: 0.8318 (ttm) cc_final: 0.8052 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.1713
  time to fit residues: 8.7014
Evaluate side-chains
  34 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3173 r_free = 0.3173 target = 0.112464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.095721 restraints weight = 3044.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.098169 restraints weight = 1732.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.099717 restraints weight = 1217.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.1179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2259  Z= 0.147
  Angle     :  0.532   7.099   3091  Z= 0.282
  Chirality :  0.040   0.105    378
  Planarity :  0.003   0.027    368
  Dihedral  :  4.595  20.606    316
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  8.00 %
    Favored  : 90.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.51), residues: 280
  helix:  1.40 (0.36), residues: 221
  sheet:  None (None), residues: 0
  loop : -0.56 (0.77), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 109 
 HIS   0.006   0.002   HIS R 178 
 PHE   0.009   0.001   PHE R  61 
 TYR   0.008   0.001   TYR R 132 
 ARG   0.001   0.000   ARG R 228 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05446 (  153)
  hydrogen bonds       : angle       4.24114 (  459)
  SS BOND              : bond        0.00264 (    2)
  SS BOND              : angle       2.23494 (    4)
  covalent geometry    : bond        0.00346 ( 2257)
  covalent geometry    : angle       0.52580 ( 3087)

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

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

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.236 
Fit side-chains
REVERT: R  279 MET cc_start: 0.8559 (mmm) cc_final: 0.8239 (mmm)
  outliers start: 3
  outliers final: 2
  residues processed: 38
  average time/residue: 0.1823
  time to fit residues: 7.9524
Evaluate side-chains
  36 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 34
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3177 r_free = 0.3177 target = 0.112640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.095508 restraints weight = 3075.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.097881 restraints weight = 1781.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.099498 restraints weight = 1254.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.1285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   2259  Z= 0.149
  Angle     :  0.526   9.469   3091  Z= 0.272
  Chirality :  0.040   0.104    378
  Planarity :  0.003   0.027    368
  Dihedral  :  4.550  17.717    316
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 2.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 10.22 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.51), residues: 280
  helix:  1.41 (0.36), residues: 221
  sheet:  None (None), residues: 0
  loop : -0.61 (0.79), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 109 
 HIS   0.007   0.002   HIS R 296 
 PHE   0.007   0.001   PHE R 332 
 TYR   0.007   0.001   TYR R 132 
 ARG   0.003   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05241 (  153)
  hydrogen bonds       : angle       4.13097 (  459)
  SS BOND              : bond        0.00364 (    2)
  SS BOND              : angle       1.38391 (    4)
  covalent geometry    : bond        0.00360 ( 2257)
  covalent geometry    : angle       0.52426 ( 3087)

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

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

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.258 
Fit side-chains
REVERT: R  279 MET cc_start: 0.8594 (mmm) cc_final: 0.8224 (mmm)
  outliers start: 5
  outliers final: 3
  residues processed: 37
  average time/residue: 0.1812
  time to fit residues: 7.7434
Evaluate side-chains
  37 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  298 ILE
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 26 optimal weight:    0.2980
   chunk 9 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0370
   chunk 27 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0370
   chunk 18 optimal weight:    0.5980
   chunk 23 optimal weight:    0.3980
   overall best weight:    0.2736

-------------------------------------------------------------------------------
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 = 0.3235 r_free = 0.3235 target = 0.116899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.099949 restraints weight = 2947.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.102397 restraints weight = 1703.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.103956 restraints weight = 1195.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   2259  Z= 0.099
  Angle     :  0.460   7.590   3091  Z= 0.241
  Chirality :  0.038   0.101    378
  Planarity :  0.003   0.025    368
  Dihedral  :  4.156  17.180    316
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 11.11 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.51), residues: 280
  helix:  1.56 (0.36), residues: 222
  sheet:  None (None), residues: 0
  loop : -0.53 (0.79), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 109 
 HIS   0.005   0.002   HIS R 178 
 PHE   0.005   0.001   PHE R  61 
 TYR   0.005   0.001   TYR R 308 
 ARG   0.004   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04157 (  153)
  hydrogen bonds       : angle       3.85805 (  459)
  SS BOND              : bond        0.00205 (    2)
  SS BOND              : angle       1.09503 (    4)
  covalent geometry    : bond        0.00204 ( 2257)
  covalent geometry    : angle       0.45892 ( 3087)

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

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

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.232 
Fit side-chains
REVERT: R  279 MET cc_start: 0.8598 (mmm) cc_final: 0.8254 (mmm)
  outliers start: 3
  outliers final: 3
  residues processed: 38
  average time/residue: 0.1662
  time to fit residues: 7.3334
Evaluate side-chains
  37 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   98 THR
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3196 r_free = 0.3196 target = 0.114108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.097192 restraints weight = 3037.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.099632 restraints weight = 1726.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.101289 restraints weight = 1219.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2259  Z= 0.144
  Angle     :  0.498   8.148   3091  Z= 0.259
  Chirality :  0.039   0.104    378
  Planarity :  0.003   0.026    368
  Dihedral  :  4.258  17.299    316
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 1.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 12.44 %
    Favored  : 85.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.51), residues: 280
  helix:  1.52 (0.36), residues: 223
  sheet:  None (None), residues: 0
  loop : -0.66 (0.79), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.005   0.002   HIS R 296 
 PHE   0.007   0.001   PHE R 332 
 TYR   0.008   0.001   TYR R 132 
 ARG   0.004   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04944 (  153)
  hydrogen bonds       : angle       3.92137 (  459)
  SS BOND              : bond        0.00147 (    2)
  SS BOND              : angle       1.35885 (    4)
  covalent geometry    : bond        0.00347 ( 2257)
  covalent geometry    : angle       0.49599 ( 3087)

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

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

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 0.238 
Fit side-chains
  outliers start: 5
  outliers final: 3
  residues processed: 38
  average time/residue: 0.1908
  time to fit residues: 8.3766
Evaluate side-chains
  38 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue   98 THR
Chi-restraints excluded: chain R residue  195 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 3 optimal weight:    0.4980
   chunk 11 optimal weight:    0.0000
   chunk 19 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 14 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.4784

-------------------------------------------------------------------------------
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 = 0.3194 r_free = 0.3194 target = 0.114282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.096915 restraints weight = 3013.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.099582 restraints weight = 1645.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.101352 restraints weight = 1125.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.1618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2259  Z= 0.116
  Angle     :  0.499  10.646   3091  Z= 0.252
  Chirality :  0.039   0.102    378
  Planarity :  0.003   0.025    368
  Dihedral  :  4.173  17.321    316
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 1.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 14.22 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.51), residues: 280
  helix:  1.60 (0.36), residues: 223
  sheet:  None (None), residues: 0
  loop : -0.79 (0.75), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 109 
 HIS   0.004   0.002   HIS R 296 
 PHE   0.007   0.001   PHE R  61 
 TYR   0.007   0.001   TYR R 132 
 ARG   0.004   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04513 (  153)
  hydrogen bonds       : angle       3.83832 (  459)
  SS BOND              : bond        0.00138 (    2)
  SS BOND              : angle       1.13575 (    4)
  covalent geometry    : bond        0.00263 ( 2257)
  covalent geometry    : angle       0.49750 ( 3087)

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

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

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.232 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 36
  average time/residue: 0.2006
  time to fit residues: 8.4007
Evaluate side-chains
  37 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   98 THR
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0060
   chunk 27 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 24 optimal weight:    6.9990
   chunk 8 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 3 optimal weight:    0.3980
   overall best weight:    0.4996

-------------------------------------------------------------------------------
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 = 0.3195 r_free = 0.3195 target = 0.113958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.096946 restraints weight = 3013.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.099474 restraints weight = 1734.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.101099 restraints weight = 1218.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2259  Z= 0.119
  Angle     :  0.500   9.794   3091  Z= 0.254
  Chirality :  0.039   0.103    378
  Planarity :  0.003   0.025    368
  Dihedral  :  4.209  17.284    316
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 2.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 14.22 %
    Favored  : 83.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.51), residues: 280
  helix:  1.58 (0.36), residues: 224
  sheet:  None (None), residues: 0
  loop : -1.00 (0.74), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.007   0.002   HIS R 296 
 PHE   0.006   0.001   PHE R  61 
 TYR   0.007   0.001   TYR R 132 
 ARG   0.005   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04540 (  153)
  hydrogen bonds       : angle       3.83944 (  459)
  SS BOND              : bond        0.00191 (    2)
  SS BOND              : angle       1.85706 (    4)
  covalent geometry    : bond        0.00274 ( 2257)
  covalent geometry    : angle       0.49585 ( 3087)

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

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

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.249 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 37
  average time/residue: 0.1757
  time to fit residues: 7.5692
Evaluate side-chains
  39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue   98 THR
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 19 optimal weight:    0.4980
   chunk 2 optimal weight:    1.9990
   chunk 10 optimal weight:    0.3980
   chunk 16 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0000
   chunk 3 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.4784

-------------------------------------------------------------------------------
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 = 0.3201 r_free = 0.3201 target = 0.114557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.097000 restraints weight = 3101.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.099689 restraints weight = 1675.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.101532 restraints weight = 1145.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2259  Z= 0.115
  Angle     :  0.490   9.290   3091  Z= 0.249
  Chirality :  0.039   0.102    378
  Planarity :  0.003   0.026    368
  Dihedral  :  4.151  17.311    316
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 14.22 %
    Favored  : 83.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.51), residues: 280
  helix:  1.64 (0.36), residues: 224
  sheet:  None (None), residues: 0
  loop : -0.91 (0.75), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.004   0.002   HIS R 296 
 PHE   0.006   0.001   PHE R  61 
 TYR   0.007   0.001   TYR R 132 
 ARG   0.006   0.001   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04471 (  153)
  hydrogen bonds       : angle       3.79320 (  459)
  SS BOND              : bond        0.00113 (    2)
  SS BOND              : angle       1.57921 (    4)
  covalent geometry    : bond        0.00263 ( 2257)
  covalent geometry    : angle       0.48713 ( 3087)

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

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

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.212 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 36
  average time/residue: 0.1694
  time to fit residues: 7.1031
Evaluate side-chains
  37 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue   98 THR
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 19 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 24 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3189 r_free = 0.3189 target = 0.113535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.096366 restraints weight = 3037.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.098919 restraints weight = 1715.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.100499 restraints weight = 1197.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.1839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2259  Z= 0.144
  Angle     :  0.516   9.193   3091  Z= 0.264
  Chirality :  0.040   0.106    378
  Planarity :  0.003   0.030    368
  Dihedral  :  4.253  17.143    316
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 14.67 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.51), residues: 280
  helix:  1.58 (0.36), residues: 224
  sheet:  None (None), residues: 0
  loop : -0.92 (0.75), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.006   0.002   HIS R 296 
 PHE   0.009   0.001   PHE R  61 
 TYR   0.010   0.001   TYR R 132 
 ARG   0.006   0.001   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04895 (  153)
  hydrogen bonds       : angle       3.87776 (  459)
  SS BOND              : bond        0.00123 (    2)
  SS BOND              : angle       1.67177 (    4)
  covalent geometry    : bond        0.00348 ( 2257)
  covalent geometry    : angle       0.51322 ( 3087)

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

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

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.237 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 36
  average time/residue: 0.1899
  time to fit residues: 7.8815
Evaluate side-chains
  38 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue   98 THR
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3177 r_free = 0.3177 target = 0.112410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.095450 restraints weight = 3039.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.097906 restraints weight = 1741.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.099572 restraints weight = 1225.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2259  Z= 0.149
  Angle     :  0.526   9.202   3091  Z= 0.270
  Chirality :  0.040   0.107    378
  Planarity :  0.003   0.032    368
  Dihedral  :  4.319  17.111    316
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 14.67 %
    Favored  : 83.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.51), residues: 280
  helix:  1.55 (0.36), residues: 224
  sheet:  None (None), residues: 0
  loop : -0.96 (0.74), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.006   0.002   HIS R 296 
 PHE   0.007   0.001   PHE R  61 
 TYR   0.011   0.001   TYR R 132 
 ARG   0.007   0.001   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05061 (  153)
  hydrogen bonds       : angle       3.93224 (  459)
  SS BOND              : bond        0.00134 (    2)
  SS BOND              : angle       1.72819 (    4)
  covalent geometry    : bond        0.00363 ( 2257)
  covalent geometry    : angle       0.52217 ( 3087)

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

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

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.240 
Fit side-chains
REVERT: R  338 GLU cc_start: 0.8343 (tt0) cc_final: 0.7962 (tt0)
  outliers start: 4
  outliers final: 4
  residues processed: 36
  average time/residue: 0.1873
  time to fit residues: 7.7932
Evaluate side-chains
  39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue   98 THR
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 5 optimal weight:    0.0570
   chunk 14 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0470
   chunk 3 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 16 optimal weight:    0.1980
   chunk 24 optimal weight:    0.7980
   chunk 20 optimal weight:    0.2980
   chunk 25 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.2796

-------------------------------------------------------------------------------
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 = 0.3214 r_free = 0.3214 target = 0.115335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.098243 restraints weight = 2991.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.100584 restraints weight = 1727.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.102316 restraints weight = 1238.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   2259  Z= 0.103
  Angle     :  0.488   8.938   3091  Z= 0.250
  Chirality :  0.039   0.102    378
  Planarity :  0.003   0.032    368
  Dihedral  :  4.195  17.179    316
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 15.11 %
    Favored  : 83.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.51), residues: 280
  helix:  1.69 (0.36), residues: 224
  sheet:  None (None), residues: 0
  loop : -0.96 (0.75), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 178 
 PHE   0.007   0.001   PHE R  61 
 TYR   0.007   0.001   TYR R 132 
 ARG   0.007   0.001   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04335 (  153)
  hydrogen bonds       : angle       3.82482 (  459)
  SS BOND              : bond        0.00123 (    2)
  SS BOND              : angle       1.47089 (    4)
  covalent geometry    : bond        0.00215 ( 2257)
  covalent geometry    : angle       0.48536 ( 3087)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1172.11 seconds
wall clock time: 21 minutes 15.69 seconds (1275.69 seconds total)