Starting phenix.real_space_refine
on Wed Mar  5 14:55:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggs_40019/03_2025/8ggs_40019.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggs_40019/03_2025/8ggs_40019.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/8ggs_40019/03_2025/8ggs_40019.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggs_40019/03_2025/8ggs_40019.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggs_40019/03_2025/8ggs_40019.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggs_40019/03_2025/8ggs_40019.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=   0.023
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    1415      2.51       5
     N     331      2.21       5
     O     353      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-5624/modules/chem_data/mon_lib"
  Total number of atoms: 2114
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2099
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2099
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 163
          Unresolved non-hydrogen angles: 200
          Unresolved non-hydrogen dihedrals: 135
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 99
    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: 2.92, per 1000 atoms: 1.38
  Number of scatterers: 2114
  At special positions: 0
  Unit cell: (56.4005, 82.4315, 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      15     16.00
     O     353      8.00
     N     331      7.00
     C    1415      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.61
  Conformation dependent library (CDL) restraints added in 296.7 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 0 sheets defined
      87.2% 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: 3.711A  pdb=" N   GLY R  37 " --> pdb=" O   VAL R  33 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 97
      removed outlier: 4.027A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 4.270A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER R 165 " --> pdb=" O   SER R 161 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 237
      removed outlier: 3.729A  pdb=" N   SER R 236 " --> pdb=" O   LYS R 232 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 287
      removed outlier: 3.877A  pdb=" N   THR R 274 " --> pdb=" O   LYS R 270 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ILE R 278 " --> pdb=" O   THR R 274 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 288 through 299
      removed outlier: 3.618A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 318
      removed outlier: 3.613A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 321 through 327
    Processing helix  chain 'R' and resid 329 through 340

    167 hydrogen bonds defined for protein.
    501 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: 0.72 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 461
        1.33 -     1.46: 511
        1.46 -     1.58: 1177
        1.58 -     1.70: 0
        1.70 -     1.82: 21
  Bond restraints: 2170
  Sorted by residual:
  bond pdb=" N   ARG R 151 "
       pdb=" CA  ARG R 151 "
    ideal  model  delta    sigma   weight residual
    1.459  1.423  0.036 1.19e-02 7.06e+03 9.18e+00
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.452 -0.055 2.00e-02 2.50e+03 7.45e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.574 -0.051 2.00e-02 2.50e+03 6.57e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.442 -0.048 2.00e-02 2.50e+03 5.75e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 2.00e-02 2.50e+03 4.89e+00
  ... (remaining 2165 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.17: 2853
        1.17 -     2.33: 98
        2.33 -     3.50: 15
        3.50 -     4.67: 7
        4.67 -     5.83: 6
  Bond angle restraints: 2979
  Sorted by residual:
  angle pdb=" C   VAL R  86 "
        pdb=" N   VAL R  87 "
        pdb=" CA  VAL R  87 "
      ideal   model   delta    sigma   weight residual
     120.33  122.51   -2.18 8.00e-01 1.56e+00 7.42e+00
  angle pdb=" C   VAL R  87 "
        pdb=" CA  VAL R  87 "
        pdb=" CB  VAL R  87 "
      ideal   model   delta    sigma   weight residual
     114.00  110.85    3.15 1.31e+00 5.83e-01 5.78e+00
  angle pdb=" N   ARG R 151 "
        pdb=" CA  ARG R 151 "
        pdb=" C   ARG R 151 "
      ideal   model   delta    sigma   weight residual
     111.07  108.90    2.17 1.07e+00 8.73e-01 4.10e+00
  angle pdb=" C   THR R  96 "
        pdb=" N   LYS R  97 "
        pdb=" CA  LYS R  97 "
      ideal   model   delta    sigma   weight residual
     124.31  127.60   -3.29 1.67e+00 3.59e-01 3.88e+00
  angle pdb=" CAE G1I R 501 "
        pdb=" CAG G1I R 501 "
        pdb=" CAH G1I R 501 "
      ideal   model   delta    sigma   weight residual
     112.63  118.12   -5.49 3.00e+00 1.11e-01 3.35e+00
  ... (remaining 2974 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.60: 1086
       12.60 -    25.19: 97
       25.19 -    37.79: 43
       37.79 -    50.38: 6
       50.38 -    62.98: 3
  Dihedral angle restraints: 1235
    sinusoidal: 407
      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 -161.65  -18.35     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CA  ALA R  85 "
           pdb=" C   ALA R  85 "
           pdb=" N   VAL R  86 "
           pdb=" CA  VAL R  86 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.54  -15.46     0      5.00e+00 4.00e-02 9.56e+00
  dihedral pdb=" CB  MET R  36 "
           pdb=" CG  MET R  36 "
           pdb=" SD  MET R  36 "
           pdb=" CE  MET R  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  117.62  -57.62     3      1.50e+01 4.44e-03 9.44e+00
  ... (remaining 1232 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 246
       0.033 -    0.066: 89
       0.066 -    0.099: 29
       0.099 -    0.132: 3
       0.132 -    0.165: 1
  Chirality restraints: 368
  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 6.78e-01
  chirality pdb=" CA  PRO R 288 "
            pdb=" N   PRO R 288 "
            pdb=" C   PRO R 288 "
            pdb=" CB  PRO R 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.10 2.00e-01 2.50e+01 2.74e-01
  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    2.62    0.10 2.00e-01 2.50e+01 2.62e-01
  ... (remaining 365 not shown)

  Planarity restraints: 357
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 167 "   -0.029 5.00e-02 4.00e+02   4.43e-02 3.14e+00
        pdb=" N   PRO R 168 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO R 168 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO R 168 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 210 "    0.016 5.00e-02 4.00e+02   2.47e-02 9.75e-01
        pdb=" N   PRO R 211 "   -0.043 5.00e-02 4.00e+02
        pdb=" CA  PRO R 211 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO R 211 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 287 "   -0.016 5.00e-02 4.00e+02   2.41e-02 9.27e-01
        pdb=" N   PRO R 288 "    0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO R 288 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO R 288 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 354 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 562
        2.81 -     3.34: 2166
        3.34 -     3.86: 3342
        3.86 -     4.38: 3425
        4.38 -     4.90: 6406
  Nonbonded interactions: 15901
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAL G1I R 501 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OH  TYR R 185 "
            pdb=" O   PHE R 194 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" OD2 ASP R 113 "
            pdb=" OAM G1I R 501 "
     model   vdw
     2.505 3.040
  nonbonded pdb=" OD1 ASN R 196 "
            pdb=" N   GLN R 197 "
     model   vdw
     2.594 3.120
  nonbonded pdb=" OG  SER R 165 "
            pdb=" N   PHE R 166 "
     model   vdw
     2.625 3.120
  ... (remaining 15896 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.030
  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:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.800
  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:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   2170  Z= 0.265
  Angle     :  0.562   5.833   2979  Z= 0.317
  Chirality :  0.038   0.165    368
  Planarity :  0.004   0.044    357
  Dihedral  : 12.384  62.978    694
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  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:  2.32 (0.50), residues: 277
  helix:  2.47 (0.35), residues: 209
  sheet:  None (None), residues: 0
  loop : -1.62 (0.71), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.007   0.001   PHE R 133 
 TYR   0.010   0.001   TYR R  70 
 ARG   0.001   0.000   ARG R  63 

*********************** 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
  32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.235 
Fit side-chains
REVERT: R   63 ARG cc_start: 0.7022 (mtm180) cc_final: 0.5599 (mpt180)
REVERT: R   84 LEU cc_start: 0.8143 (mm) cc_final: 0.7740 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.2166
  time to fit residues: 7.9416
Evaluate side-chains
  24 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 21 optimal weight:    0.0050
   chunk 11 optimal weight:    0.7980
   chunk 7 optimal weight:    0.4980
   chunk 14 optimal weight:    0.1980
   chunk 8 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.4194

-------------------------------------------------------------------------------
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 = 0.3464 r_free = 0.3464 target = 0.131926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.117754 restraints weight = 3019.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.120403 restraints weight = 1534.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.122223 restraints weight = 964.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.1144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   2170  Z= 0.159
  Angle     :  0.466   4.848   2979  Z= 0.258
  Chirality :  0.038   0.110    368
  Planarity :  0.003   0.026    357
  Dihedral  :  4.257  18.020    309
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 10.19 %
    Favored  : 87.86 %
  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:  2.55 (0.50), residues: 277
  helix:  2.55 (0.34), residues: 222
  sheet:  None (None), residues: 0
  loop : -2.21 (0.68), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 313 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.008   0.001   PHE R 282 
 TYR   0.007   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R  63 

*********************** 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
  35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.245 
Fit side-chains
REVERT: R   63 ARG cc_start: 0.7189 (mtm180) cc_final: 0.5675 (mpt180)
REVERT: R   84 LEU cc_start: 0.8150 (mm) cc_final: 0.7612 (mm)
REVERT: R  151 ARG cc_start: 0.7516 (mtm-85) cc_final: 0.6434 (mmt-90)
REVERT: R  205 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7573 (mp)
  outliers start: 4
  outliers final: 3
  residues processed: 34
  average time/residue: 0.1941
  time to fit residues: 7.6498
Evaluate side-chains
  30 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue  182 ILE
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  233 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 15 optimal weight:    0.5980
   chunk 18 optimal weight:    0.4980
   chunk 9 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0970
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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 = 0.3436 r_free = 0.3436 target = 0.129162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.115185 restraints weight = 3021.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.117635 restraints weight = 1569.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.119426 restraints weight = 1007.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.1401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2170  Z= 0.171
  Angle     :  0.454   5.190   2979  Z= 0.251
  Chirality :  0.038   0.112    368
  Planarity :  0.003   0.026    357
  Dihedral  :  4.331  17.762    309
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 1.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 13.11 %
    Favored  : 83.50 %
  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:  2.74 (0.50), residues: 277
  helix:  2.72 (0.34), residues: 222
  sheet:  None (None), residues: 0
  loop : -2.27 (0.65), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R 313 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.008   0.001   PHE R 282 
 TYR   0.006   0.001   TYR R 308 
 ARG   0.002   0.000   ARG R 151 

*********************** 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
  33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 26
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: R   63 ARG cc_start: 0.7319 (mtm180) cc_final: 0.5607 (mpt180)
REVERT: R   84 LEU cc_start: 0.8182 (mm) cc_final: 0.7627 (mm)
REVERT: R  205 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7634 (mp)
  outliers start: 7
  outliers final: 6
  residues processed: 31
  average time/residue: 0.2199
  time to fit residues: 7.8960
Evaluate side-chains
  31 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 24
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  233 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 1 optimal weight:    0.4980
   chunk 8 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3398 r_free = 0.3398 target = 0.125779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.111684 restraints weight = 3072.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.114126 restraints weight = 1623.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.115811 restraints weight = 1045.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2170  Z= 0.204
  Angle     :  0.469   5.310   2979  Z= 0.263
  Chirality :  0.038   0.113    368
  Planarity :  0.003   0.027    357
  Dihedral  :  4.363  17.664    309
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 1.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 14.56 %
    Favored  : 81.55 %
  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:  2.68 (0.50), residues: 277
  helix:  2.76 (0.34), residues: 220
  sheet:  None (None), residues: 0
  loop : -2.51 (0.63), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R 282 
 TYR   0.007   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R  63 

*********************** 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
  33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 25
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: R   63 ARG cc_start: 0.7474 (mtm180) cc_final: 0.5735 (mmt180)
REVERT: R   84 LEU cc_start: 0.8213 (mm) cc_final: 0.7606 (mm)
REVERT: R  151 ARG cc_start: 0.7436 (mtm-85) cc_final: 0.6461 (mmt-90)
REVERT: R  205 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7635 (mp)
  outliers start: 8
  outliers final: 6
  residues processed: 31
  average time/residue: 0.2379
  time to fit residues: 8.5484
Evaluate side-chains
  31 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 24
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3394 r_free = 0.3394 target = 0.125463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.111401 restraints weight = 3084.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.113817 restraints weight = 1635.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.115492 restraints weight = 1054.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2170  Z= 0.206
  Angle     :  0.466   5.327   2979  Z= 0.261
  Chirality :  0.038   0.114    368
  Planarity :  0.003   0.028    357
  Dihedral  :  4.388  17.789    309
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 1.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 17.48 %
    Favored  : 79.13 %
  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:  2.68 (0.50), residues: 277
  helix:  2.76 (0.34), residues: 220
  sheet:  None (None), residues: 0
  loop : -2.53 (0.61), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R 282 
 TYR   0.007   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R  63 

*********************** 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
  32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 25
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
REVERT: R   63 ARG cc_start: 0.7562 (mtm180) cc_final: 0.5723 (mmt180)
REVERT: R   84 LEU cc_start: 0.8199 (mm) cc_final: 0.7604 (mm)
REVERT: R  151 ARG cc_start: 0.7426 (mtm-85) cc_final: 0.6461 (mmt-90)
REVERT: R  205 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7646 (mp)
  outliers start: 7
  outliers final: 5
  residues processed: 31
  average time/residue: 0.1880
  time to fit residues: 6.8074
Evaluate side-chains
  31 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 25
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  233 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 10 optimal weight:    0.3980
   chunk 12 optimal weight:    0.8980
   chunk 7 optimal weight:    0.2980
   chunk 21 optimal weight:    0.8980
   chunk 27 optimal weight:    0.1980
   chunk 9 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.3430 r_free = 0.3430 target = 0.128214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.114059 restraints weight = 3078.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.116533 restraints weight = 1615.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.118311 restraints weight = 1037.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   2170  Z= 0.154
  Angle     :  0.428   5.282   2979  Z= 0.239
  Chirality :  0.037   0.107    368
  Planarity :  0.003   0.028    357
  Dihedral  :  4.235  17.533    309
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 17.48 %
    Favored  : 78.16 %
  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:  2.79 (0.50), residues: 277
  helix:  2.77 (0.34), residues: 222
  sheet:  None (None), residues: 0
  loop : -2.37 (0.63), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R  93 
 PHE   0.007   0.001   PHE R 282 
 TYR   0.006   0.001   TYR R 308 
 ARG   0.002   0.000   ARG R 175 

*********************** 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
  35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 26
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: R   63 ARG cc_start: 0.7604 (mtm180) cc_final: 0.5663 (mmt180)
REVERT: R   84 LEU cc_start: 0.8011 (mm) cc_final: 0.7376 (mm)
REVERT: R  151 ARG cc_start: 0.7332 (mtm-85) cc_final: 0.6271 (mmt-90)
REVERT: R  205 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7485 (mp)
  outliers start: 9
  outliers final: 6
  residues processed: 34
  average time/residue: 0.1874
  time to fit residues: 7.3604
Evaluate side-chains
  32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 25
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  233 ILE
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 3 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0770
   chunk 2 optimal weight:    0.9990
   chunk 5 optimal weight:    0.2980
   chunk 23 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 6 optimal weight:    0.1980
   chunk 15 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.3938

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.128093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.113916 restraints weight = 3092.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.116419 restraints weight = 1645.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.118167 restraints weight = 1056.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.1761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2170  Z= 0.168
  Angle     :  0.444   5.307   2979  Z= 0.247
  Chirality :  0.038   0.110    368
  Planarity :  0.003   0.027    357
  Dihedral  :  4.217  17.517    309
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 19.90 %
    Favored  : 76.21 %
  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:  2.86 (0.51), residues: 277
  helix:  2.84 (0.34), residues: 222
  sheet:  None (None), residues: 0
  loop : -2.41 (0.63), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP R 109 
 HIS   0.006   0.002   HIS R 296 
 PHE   0.007   0.001   PHE R 282 
 TYR   0.007   0.001   TYR R 185 
 ARG   0.001   0.000   ARG R 151 

*********************** 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
  32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 24
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: R   63 ARG cc_start: 0.7634 (mtm180) cc_final: 0.5706 (mmt180)
REVERT: R   84 LEU cc_start: 0.7925 (mm) cc_final: 0.7289 (mm)
REVERT: R  151 ARG cc_start: 0.7309 (mtm-85) cc_final: 0.6191 (mmt-90)
REVERT: R  205 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7425 (mp)
  outliers start: 8
  outliers final: 5
  residues processed: 29
  average time/residue: 0.1896
  time to fit residues: 6.3888
Evaluate side-chains
  28 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  233 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 15 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 3 optimal weight:    0.5980
   chunk 11 optimal weight:    0.0970
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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 = 0.3412 r_free = 0.3412 target = 0.126603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.112355 restraints weight = 3196.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.114801 restraints weight = 1700.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.116606 restraints weight = 1097.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2170  Z= 0.185
  Angle     :  0.454   5.322   2979  Z= 0.255
  Chirality :  0.038   0.113    368
  Planarity :  0.003   0.027    357
  Dihedral  :  4.256  17.475    309
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 19.42 %
    Favored  : 76.21 %
  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:  2.87 (0.50), residues: 277
  helix:  2.92 (0.34), residues: 220
  sheet:  None (None), residues: 0
  loop : -2.58 (0.60), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R 109 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.008   0.001   PHE R 282 
 TYR   0.007   0.001   TYR R 308 
 ARG   0.002   0.000   ARG R  63 

*********************** 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
  32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 23
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: R   63 ARG cc_start: 0.7677 (mtm180) cc_final: 0.5905 (mmt180)
REVERT: R   84 LEU cc_start: 0.8183 (mm) cc_final: 0.7573 (mm)
REVERT: R  151 ARG cc_start: 0.7352 (mtm-85) cc_final: 0.6416 (mmt-90)
REVERT: R  205 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7733 (mp)
  outliers start: 9
  outliers final: 6
  residues processed: 30
  average time/residue: 0.2342
  time to fit residues: 8.1110
Evaluate side-chains
  30 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 23
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain R residue  126 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
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 19 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 2 optimal weight:    0.4980
   chunk 11 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.126060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.112027 restraints weight = 3098.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.114380 restraints weight = 1661.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.116110 restraints weight = 1079.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
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      :  0.003   0.026   2170  Z= 0.202
  Angle     :  0.465   5.327   2979  Z= 0.260
  Chirality :  0.038   0.115    368
  Planarity :  0.003   0.027    357
  Dihedral  :  4.272  17.511    309
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 20.39 %
    Favored  : 75.73 %
  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:  2.82 (0.50), residues: 277
  helix:  2.88 (0.34), residues: 220
  sheet:  None (None), residues: 0
  loop : -2.56 (0.60), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R 109 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.008   0.001   PHE R 282 
 TYR   0.007   0.001   TYR R 308 
 ARG   0.002   0.000   ARG R  63 

*********************** 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
  30 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 22
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
REVERT: R   63 ARG cc_start: 0.7668 (mtm180) cc_final: 0.5795 (mmt180)
REVERT: R   84 LEU cc_start: 0.7960 (mm) cc_final: 0.7324 (mm)
REVERT: R  151 ARG cc_start: 0.7336 (mtm-85) cc_final: 0.6224 (mmt-90)
REVERT: R  205 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7438 (mp)
  outliers start: 8
  outliers final: 5
  residues processed: 28
  average time/residue: 0.2137
  time to fit residues: 6.9563
Evaluate side-chains
  28 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain R residue  126 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0980
   chunk 17 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0020
   chunk 20 optimal weight:    0.9990
   chunk 26 optimal weight:    0.3980
   chunk 7 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0980
   overall best weight:    0.2388

-------------------------------------------------------------------------------
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 = 0.3483 r_free = 0.3483 target = 0.132405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.117827 restraints weight = 3037.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.120607 restraints weight = 1552.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.122534 restraints weight = 972.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   2170  Z= 0.128
  Angle     :  0.426   5.305   2979  Z= 0.233
  Chirality :  0.037   0.103    368
  Planarity :  0.003   0.027    357
  Dihedral  :  4.003  17.377    309
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 20.87 %
    Favored  : 75.73 %
  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:  3.00 (0.50), residues: 277
  helix:  2.96 (0.34), residues: 222
  sheet:  None (None), residues: 0
  loop : -2.47 (0.60), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.002   0.001   HIS R  93 
 PHE   0.006   0.001   PHE R  61 
 TYR   0.005   0.001   TYR R 209 
 ARG   0.001   0.000   ARG R 151 

********************** 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
  30 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 23
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: R   63 ARG cc_start: 0.7609 (mtm180) cc_final: 0.5808 (mmt180)
REVERT: R   84 LEU cc_start: 0.7894 (mm) cc_final: 0.7259 (mm)
REVERT: R  151 ARG cc_start: 0.7221 (mtm-85) cc_final: 0.6115 (mmt-90)
REVERT: R  205 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7537 (mp)
  outliers start: 7
  outliers final: 5
  residues processed: 28
  average time/residue: 0.1852
  time to fit residues: 6.1239
Evaluate side-chains
  28 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain R residue  126 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  205 ILE
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 18 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3396 r_free = 0.3396 target = 0.125150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.110710 restraints weight = 3139.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.113146 restraints weight = 1671.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.114916 restraints weight = 1082.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2170  Z= 0.251
  Angle     :  0.497   5.687   2979  Z= 0.277
  Chirality :  0.040   0.120    368
  Planarity :  0.003   0.028    357
  Dihedral  :  4.249  17.495    309
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 21.36 %
    Favored  : 75.24 %
  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:  2.85 (0.50), residues: 277
  helix:  2.92 (0.34), residues: 220
  sheet:  None (None), residues: 0
  loop : -2.65 (0.59), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP R 109 
 HIS   0.010   0.003   HIS R 296 
 PHE   0.010   0.001   PHE R 282 
 TYR   0.007   0.001   TYR R 308 
 ARG   0.003   0.001   ARG R  63 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1228.75 seconds
wall clock time: 21 minutes 56.31 seconds (1316.31 seconds total)