Starting phenix.real_space_refine
on Mon Feb 10 19:58:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggy_40025/02_2025/8ggy_40025.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggy_40025/02_2025/8ggy_40025.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ggy_40025/02_2025/8ggy_40025.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggy_40025/02_2025/8ggy_40025.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggy_40025/02_2025/8ggy_40025.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggy_40025/02_2025/8ggy_40025.cif"
  }
  resolution = 3.9
  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=   0.018
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      13      5.16       5
     C    1388      2.51       5
     N     339      2.21       5
     O     356      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 2096
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2081
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2081
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 55}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 182
          Unresolved non-hydrogen angles: 228
          Unresolved non-hydrogen dihedrals: 147
          Unresolved non-hydrogen chiralities: 23
          Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 6, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 73
    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: 3.15, per 1000 atoms: 1.50
  Number of scatterers: 2096
  At special positions: 0
  Unit cell: (54.6651, 85.9023, 62.4744, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      13     16.00
     O     356      8.00
     N     339      7.00
     C    1388      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.18
  Conformation dependent library (CDL) restraints added in 903.1 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 0 sheets defined
      85.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 3.619A  pdb=" N   MET R  36 " --> pdb=" O   TRP R  32 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 69 through 86
    Processing helix  chain 'R' and resid 86 through 96
    Processing helix  chain 'R' and resid 103 through 137
      removed outlier: 4.335A  pdb=" N   GLU R 107 " --> pdb=" O   ASN R 103 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   PHE R 108 " --> pdb=" O   PHE R 104 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ARG R 131 " --> pdb=" O   ILE R 127 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 164
      removed outlier: 3.690A  pdb=" N   ALA R 150 " --> pdb=" O   THR R 146 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 166 through 171
      removed outlier: 3.760A  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: 3.719A  pdb=" N   ALA R 200 " --> pdb=" O   ASN R 196 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ILE R 201 " --> pdb=" O   GLN R 197 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 237
    Processing helix  chain 'R' and resid 270 through 299
      removed outlier: 3.788A  pdb=" N   THR R 274 " --> pdb=" O   LYS R 270 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.774A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 305 through 316
    Processing helix  chain 'R' and resid 317 through 327
      removed outlier: 3.584A  pdb=" N   PHE R 321 " --> pdb=" O   VAL R 317 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 340
      removed outlier: 3.513A  pdb=" N   LEU R 340 " --> pdb=" O   PHE R 336 " (cutoff:3.500A)

    160 hydrogen bonds defined for protein.
    480 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: 0.69 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: 643
        1.34 -     1.46: 589
        1.46 -     1.58: 900
        1.58 -     1.70: 0
        1.70 -     1.82: 19
  Bond restraints: 2151
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.453 -0.056 2.00e-02 2.50e+03 7.78e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.578 -0.055 2.00e-02 2.50e+03 7.56e+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 6.08e+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 5.51e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" NAN G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.451  1.497 -0.046 2.00e-02 2.50e+03 5.21e+00
  ... (remaining 2146 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 2843
        1.38 -     2.75: 77
        2.75 -     4.13: 19
        4.13 -     5.51: 10
        5.51 -     6.88: 2
  Bond angle restraints: 2951
  Sorted by residual:
  angle pdb=" C   GLU R 180 "
        pdb=" N   ALA R 181 "
        pdb=" CA  ALA R 181 "
      ideal   model   delta    sigma   weight residual
     121.54  128.17   -6.63 1.91e+00 2.74e-01 1.21e+01
  angle pdb=" C   VAL R 295 "
        pdb=" N   HIS R 296 "
        pdb=" CA  HIS R 296 "
      ideal   model   delta    sigma   weight residual
     120.72  116.07    4.65 1.67e+00 3.59e-01 7.75e+00
  angle pdb=" CB  MET R 279 "
        pdb=" CG  MET R 279 "
        pdb=" SD  MET R 279 "
      ideal   model   delta    sigma   weight residual
     112.70  119.58   -6.88 3.00e+00 1.11e-01 5.26e+00
  angle pdb=" CA  GLN R 337 "
        pdb=" CB  GLN R 337 "
        pdb=" CG  GLN R 337 "
      ideal   model   delta    sigma   weight residual
     114.10  118.62   -4.52 2.00e+00 2.50e-01 5.10e+00
  angle pdb=" C   ASP R 300 "
        pdb=" N   ASN R 301 "
        pdb=" CA  ASN R 301 "
      ideal   model   delta    sigma   weight residual
     123.05  126.33   -3.28 1.57e+00 4.06e-01 4.36e+00
  ... (remaining 2946 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.70: 1088
       15.70 -    31.39: 95
       31.39 -    47.09: 32
       47.09 -    62.78: 5
       62.78 -    78.48: 4
  Dihedral angle restraints: 1224
    sinusoidal: 396
      harmonic: 828
  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 -164.67  -15.33     0      5.00e+00 4.00e-02 9.40e+00
  dihedral pdb=" CA  ARG R 131 "
           pdb=" CB  ARG R 131 "
           pdb=" CG  ARG R 131 "
           pdb=" CD  ARG R 131 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -126.96  -53.04     3      1.50e+01 4.44e-03 9.17e+00
  dihedral pdb=" CA  ILE R 325 "
           pdb=" C   ILE R 325 "
           pdb=" N   TYR R 326 "
           pdb=" CA  TYR R 326 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -165.11  -14.89     0      5.00e+00 4.00e-02 8.87e+00
  ... (remaining 1221 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 237
       0.035 -    0.069: 91
       0.069 -    0.103: 22
       0.103 -    0.138: 3
       0.138 -    0.172: 1
  Chirality restraints: 354
  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 7.43e-01
  chirality pdb=" CA  ILE R 303 "
            pdb=" N   ILE R 303 "
            pdb=" C   ILE R 303 "
            pdb=" CB  ILE R 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.40e-01
  chirality pdb=" CB  VAL R 295 "
            pdb=" CA  VAL R 295 "
            pdb=" CG1 VAL R 295 "
            pdb=" CG2 VAL R 295 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 4.18e-01
  ... (remaining 351 not shown)

  Planarity restraints: 363
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER R 329 "   -0.029 5.00e-02 4.00e+02   4.39e-02 3.08e+00
        pdb=" N   PRO R 330 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO R 330 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO R 330 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA R 198 "   -0.006 2.00e-02 2.50e+03   1.14e-02 1.31e+00
        pdb=" C   ALA R 198 "    0.020 2.00e-02 2.50e+03
        pdb=" O   ALA R 198 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   TYR R 199 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 281 "   -0.004 2.00e-02 2.50e+03   8.53e-03 7.27e-01
        pdb=" C   THR R 281 "    0.015 2.00e-02 2.50e+03
        pdb=" O   THR R 281 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   PHE R 282 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 360 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.88: 784
        2.88 -     3.39: 2232
        3.39 -     3.89: 3300
        3.89 -     4.40: 3172
        4.40 -     4.90: 5820
  Nonbonded interactions: 15308
  Sorted by model distance:
  nonbonded pdb=" O   ALA R  92 "
            pdb=" OG1 THR R  96 "
     model   vdw
     2.377 3.040
  nonbonded pdb=" O   TRP R  99 "
            pdb=" OG1 THR R 100 "
     model   vdw
     2.438 3.040
  nonbonded pdb=" OD1 ASP R 130 "
            pdb=" N   ARG R 131 "
     model   vdw
     2.481 3.120
  nonbonded pdb=" O   GLN R 337 "
            pdb=" OE1 GLN R 337 "
     model   vdw
     2.559 3.040
  nonbonded pdb=" O   ILE R 127 "
            pdb=" OD1 ASP R 130 "
     model   vdw
     2.585 3.040
  ... (remaining 15303 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:             1.920
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     11.820
  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:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
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   0.056   2151  Z= 0.242
  Angle     :  0.631   6.883   2951  Z= 0.330
  Chirality :  0.040   0.172    354
  Planarity :  0.004   0.044    363
  Dihedral  : 14.743  78.477    686
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  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:  2.19 (0.51), residues: 277
  helix:  2.21 (0.36), residues: 217
  sheet:  None (None), residues: 0
  loop : -1.51 (0.67), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 109 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R 290 
 TYR   0.006   0.001   TYR R 326 
 ARG   0.003   0.000   ARG R 228 

*********************** 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
  45 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.237 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.1352
  time to fit residues: 7.3723
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  : 0.231 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0370
   chunk 25 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.5658

-------------------------------------------------------------------------------
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 = 0.3468 r_free = 0.3468 target = 0.129182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.116007 restraints weight = 3724.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.118785 restraints weight = 1993.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.120787 restraints weight = 1226.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.1234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2151  Z= 0.178
  Angle     :  0.558   5.821   2951  Z= 0.298
  Chirality :  0.040   0.131    354
  Planarity :  0.004   0.042    363
  Dihedral  :  3.928  15.373    312
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 10.88 %
    Favored  : 85.49 %
  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:  2.17 (0.51), residues: 277
  helix:  2.04 (0.35), residues: 224
  sheet:  None (None), residues: 0
  loop : -1.23 (0.70), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 109 
 HIS   0.001   0.001   HIS R 296 
 PHE   0.017   0.001   PHE R 104 
 TYR   0.018   0.001   TYR R 308 
 ARG   0.004   0.001   ARG R 228 

*********************** 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
  43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.231 
Fit side-chains
REVERT: R  339 LEU cc_start: 0.8498 (mm) cc_final: 0.8216 (mm)
  outliers start: 7
  outliers final: 5
  residues processed: 40
  average time/residue: 0.1320
  time to fit residues: 6.4738
Evaluate side-chains
  36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   52 VAL
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  329 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 11 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 = 0.3505 r_free = 0.3505 target = 0.132311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.119398 restraints weight = 3607.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.122011 restraints weight = 1969.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.123899 restraints weight = 1234.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2151  Z= 0.207
  Angle     :  0.564   5.064   2951  Z= 0.307
  Chirality :  0.040   0.131    354
  Planarity :  0.004   0.040    363
  Dihedral  :  4.090  15.365    312
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 1.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 15.03 %
    Favored  : 79.79 %
  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:  1.99 (0.50), residues: 277
  helix:  1.93 (0.35), residues: 224
  sheet:  None (None), residues: 0
  loop : -1.37 (0.71), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 109 
 HIS   0.001   0.001   HIS R 296 
 PHE   0.018   0.001   PHE R 104 
 TYR   0.014   0.001   TYR R 308 
 ARG   0.003   0.000   ARG R 228 

*********************** 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
  42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 32
  time to evaluate  : 0.231 
Fit side-chains
REVERT: R  339 LEU cc_start: 0.8554 (mm) cc_final: 0.8269 (mm)
  outliers start: 10
  outliers final: 8
  residues processed: 39
  average time/residue: 0.1265
  time to fit residues: 5.9743
Evaluate side-chains
  36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 28
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   52 VAL
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  127 ILE
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  324 LEU
Chi-restraints excluded: chain R residue  329 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 18 optimal weight:    0.3980
   chunk 17 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 16 optimal weight:    0.2980
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.127798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.114786 restraints weight = 3777.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.117495 restraints weight = 2045.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.119500 restraints weight = 1277.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2151  Z= 0.170
  Angle     :  0.551   6.504   2951  Z= 0.293
  Chirality :  0.040   0.133    354
  Planarity :  0.004   0.040    363
  Dihedral  :  3.964  15.392    312
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 18.13 %
    Favored  : 76.68 %
  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:  2.17 (0.51), residues: 277
  helix:  2.04 (0.35), residues: 225
  sheet:  None (None), residues: 0
  loop : -1.28 (0.71), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 109 
 HIS   0.001   0.000   HIS R 296 
 PHE   0.014   0.001   PHE R 104 
 TYR   0.012   0.001   TYR R 308 
 ARG   0.004   0.000   ARG R 228 

*********************** 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
  39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 29
  time to evaluate  : 0.224 
Fit side-chains
REVERT: R  339 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8176 (mt)
  outliers start: 10
  outliers final: 8
  residues processed: 34
  average time/residue: 0.1373
  time to fit residues: 5.6110
Evaluate side-chains
  37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   52 VAL
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  127 ILE
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  279 MET
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  329 SER
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 14 optimal weight:    0.4980
   chunk 21 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3512 r_free = 0.3512 target = 0.132520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.119468 restraints weight = 3677.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.122119 restraints weight = 2013.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.124033 restraints weight = 1261.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2151  Z= 0.192
  Angle     :  0.555   5.179   2951  Z= 0.302
  Chirality :  0.040   0.132    354
  Planarity :  0.004   0.040    363
  Dihedral  :  4.007  15.635    312
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 1.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  6.74 %
    Allowed  : 16.58 %
    Favored  : 76.68 %
  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:  2.13 (0.51), residues: 277
  helix:  2.08 (0.35), residues: 223
  sheet:  None (None), residues: 0
  loop : -1.54 (0.71), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 109 
 HIS   0.001   0.001   HIS R 296 
 PHE   0.011   0.001   PHE R 104 
 TYR   0.013   0.001   TYR R 308 
 ARG   0.004   0.000   ARG R 228 

*********************** 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
  43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 30
  time to evaluate  : 0.218 
Fit side-chains
REVERT: R  339 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8146 (mt)
  outliers start: 13
  outliers final: 9
  residues processed: 38
  average time/residue: 0.1309
  time to fit residues: 5.9709
Evaluate side-chains
  40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 30
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   52 VAL
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  127 ILE
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  279 MET
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  324 LEU
Chi-restraints excluded: chain R residue  329 SER
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 18 optimal weight:    0.3980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3422 r_free = 0.3422 target = 0.125591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.112630 restraints weight = 3811.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.115335 restraints weight = 2077.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.117179 restraints weight = 1300.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2151  Z= 0.191
  Angle     :  0.558   5.798   2951  Z= 0.301
  Chirality :  0.040   0.132    354
  Planarity :  0.004   0.039    363
  Dihedral  :  3.999  15.667    312
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 1.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 18.13 %
    Favored  : 76.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.16 (0.51), residues: 277
  helix:  2.03 (0.35), residues: 225
  sheet:  None (None), residues: 0
  loop : -1.30 (0.72), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 109 
 HIS   0.001   0.001   HIS R 296 
 PHE   0.011   0.001   PHE R 104 
 TYR   0.013   0.001   TYR R 308 
 ARG   0.003   0.000   ARG R 228 

*********************** 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
  42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 31
  time to evaluate  : 0.215 
Fit side-chains
REVERT: R  339 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8180 (mt)
  outliers start: 11
  outliers final: 8
  residues processed: 37
  average time/residue: 0.1285
  time to fit residues: 5.7087
Evaluate side-chains
  39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 30
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   52 VAL
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  127 ILE
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  279 MET
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  329 SER
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 1 optimal weight:    4.9990
   chunk 3 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0070
   chunk 17 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.4998

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.127052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.114088 restraints weight = 3805.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.116852 restraints weight = 2057.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.118834 restraints weight = 1284.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2151  Z= 0.165
  Angle     :  0.551   6.116   2951  Z= 0.293
  Chirality :  0.039   0.131    354
  Planarity :  0.004   0.039    363
  Dihedral  :  3.905  15.653    312
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 18.65 %
    Favored  : 76.68 %
  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:  2.26 (0.51), residues: 277
  helix:  2.09 (0.35), residues: 226
  sheet:  None (None), residues: 0
  loop : -1.29 (0.73), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 109 
 HIS   0.001   0.001   HIS R 296 
 PHE   0.010   0.001   PHE R 104 
 TYR   0.012   0.001   TYR R 308 
 ARG   0.004   0.000   ARG R 228 

*********************** 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
  43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 34
  time to evaluate  : 0.236 
Fit side-chains
REVERT: R  339 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8173 (mt)
  outliers start: 9
  outliers final: 8
  residues processed: 38
  average time/residue: 0.1281
  time to fit residues: 5.8883
Evaluate side-chains
  42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 33
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   52 VAL
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  127 ILE
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  279 MET
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  329 SER
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 13 optimal weight:    0.5980
   chunk 3 optimal weight:    0.4980
   chunk 19 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3411 r_free = 0.3411 target = 0.124780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.111776 restraints weight = 3867.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.114525 restraints weight = 2101.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.116369 restraints weight = 1306.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2151  Z= 0.196
  Angle     :  0.577   6.404   2951  Z= 0.307
  Chirality :  0.040   0.131    354
  Planarity :  0.004   0.039    363
  Dihedral  :  3.996  15.639    312
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 18.65 %
    Favored  : 76.68 %
  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:  2.14 (0.50), residues: 277
  helix:  2.07 (0.35), residues: 223
  sheet:  None (None), residues: 0
  loop : -1.43 (0.70), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 109 
 HIS   0.001   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R 104 
 TYR   0.013   0.001   TYR R 308 
 ARG   0.004   0.000   ARG R 228 

*********************** 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
  39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 30
  time to evaluate  : 0.210 
Fit side-chains
REVERT: R  339 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8137 (mt)
  outliers start: 9
  outliers final: 8
  residues processed: 35
  average time/residue: 0.1366
  time to fit residues: 5.7304
Evaluate side-chains
  39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 30
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   52 VAL
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  127 ILE
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  279 MET
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  329 SER
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 0 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   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 = 0.3396 r_free = 0.3396 target = 0.123589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.110751 restraints weight = 3894.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.113401 restraints weight = 2113.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.115304 restraints weight = 1324.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2151  Z= 0.207
  Angle     :  0.589   6.807   2951  Z= 0.314
  Chirality :  0.040   0.131    354
  Planarity :  0.004   0.039    363
  Dihedral  :  4.082  15.634    312
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 18.65 %
    Favored  : 76.68 %
  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:  2.09 (0.50), residues: 277
  helix:  2.03 (0.35), residues: 223
  sheet:  None (None), residues: 0
  loop : -1.44 (0.70), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 109 
 HIS   0.001   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R 104 
 TYR   0.013   0.001   TYR R 308 
 ARG   0.004   0.000   ARG R 228 

*********************** 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
  40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.235 
Fit side-chains
REVERT: R  339 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8163 (mt)
  outliers start: 9
  outliers final: 8
  residues processed: 36
  average time/residue: 0.1300
  time to fit residues: 5.6640
Evaluate side-chains
  40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   52 VAL
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  127 ILE
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  279 MET
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  329 SER
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0980
   chunk 24 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0270
   chunk 22 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.5038

-------------------------------------------------------------------------------
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 = 0.3422 r_free = 0.3422 target = 0.126077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.113335 restraints weight = 3777.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.116101 restraints weight = 2051.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.118046 restraints weight = 1273.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2151  Z= 0.174
  Angle     :  0.580   7.263   2951  Z= 0.307
  Chirality :  0.040   0.131    354
  Planarity :  0.004   0.039    363
  Dihedral  :  3.946  15.633    312
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 18.65 %
    Favored  : 76.68 %
  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:  2.25 (0.51), residues: 277
  helix:  2.12 (0.35), residues: 224
  sheet:  None (None), residues: 0
  loop : -1.30 (0.77), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 109 
 HIS   0.001   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R 104 
 TYR   0.012   0.001   TYR R 308 
 ARG   0.004   0.000   ARG R 228 

********************** 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
  41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.230 
Fit side-chains
REVERT: R  339 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8178 (mt)
  outliers start: 9
  outliers final: 8
  residues processed: 36
  average time/residue: 0.1326
  time to fit residues: 5.7730
Evaluate side-chains
  41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   52 VAL
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  127 ILE
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  279 MET
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  329 SER
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 18 optimal weight:    0.0050
   chunk 9 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0870
   chunk 2 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.4572

-------------------------------------------------------------------------------
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 = 0.3437 r_free = 0.3437 target = 0.127332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.114591 restraints weight = 3811.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.117390 restraints weight = 2046.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.119395 restraints weight = 1267.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2151  Z= 0.165
  Angle     :  0.571   7.067   2951  Z= 0.301
  Chirality :  0.039   0.131    354
  Planarity :  0.004   0.039    363
  Dihedral  :  3.881  15.624    312
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 19.17 %
    Favored  : 76.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.31 (0.51), residues: 277
  helix:  2.16 (0.35), residues: 224
  sheet:  None (None), residues: 0
  loop : -1.31 (0.76), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 109 
 HIS   0.001   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R 104 
 TYR   0.012   0.001   TYR R 308 
 ARG   0.004   0.000   ARG R 228 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1043.51 seconds
wall clock time: 19 minutes 21.16 seconds (1161.16 seconds total)