Starting phenix.real_space_refine
on Mon Feb 10 20:04:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggq_40017/02_2025/8ggq_40017.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggq_40017/02_2025/8ggq_40017.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ggq_40017/02_2025/8ggq_40017.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggq_40017/02_2025/8ggq_40017.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggq_40017/02_2025/8ggq_40017.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggq_40017/02_2025/8ggq_40017.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      13      5.16       5
     C    1421      2.51       5
     N     342      2.21       5
     O     354      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: 2130
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2115
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 148
          Unresolved non-hydrogen angles: 182
          Unresolved non-hydrogen dihedrals: 124
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 82
    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: 2.62, per 1000 atoms: 1.23
  Number of scatterers: 2130
  At special positions: 0
  Unit cell: (56.4005, 82.4315, 63.3421, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      13     16.00
     O     354      8.00
     N     342      7.00
     C    1421      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: 0.56
  Conformation dependent library (CDL) restraints added in 637.8 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:
      11 helices and 0 sheets defined
      87.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 4.200A  pdb=" N   GLY R  37 " --> pdb=" O   VAL R  33 " (cutoff:3.500A)
      removed outlier: 5.709A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   MET R  40 " --> pdb=" O   MET R  36 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 97
      removed outlier: 3.881A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.651A  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
      removed outlier: 3.562A  pdb=" N   SER R 137 " --> pdb=" O   PHE R 133 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 4.030A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 4.333A  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
      removed outlier: 3.648A  pdb=" N   ILE R 182 " --> pdb=" O   HIS R 178 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ASN R 183 " --> pdb=" O   GLN R 179 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 236
    Processing helix  chain 'R' and resid 270 through 299
      removed outlier: 3.936A  pdb=" N   THR R 274 " --> pdb=" O   LYS R 270 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.658A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ILE R 298 " --> pdb=" O   ILE R 294 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 327
      removed outlier: 3.597A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   PHE R 321 " --> pdb=" O   VAL R 317 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ASN R 322 " --> pdb=" O   ASN R 318 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 340

    166 hydrogen bonds defined for protein.
    498 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: 0.57 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: 637
        1.34 -     1.46: 456
        1.46 -     1.57: 1074
        1.57 -     1.69: 1
        1.69 -     1.81: 17
  Bond restraints: 2185
  Sorted by residual:
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.576 -0.053 2.00e-02 2.50e+03 6.99e+00
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.450 -0.053 2.00e-02 2.50e+03 6.93e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.440 -0.046 2.00e-02 2.50e+03 5.30e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.562 -0.042 2.00e-02 2.50e+03 4.47e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" NAN G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.451  1.484 -0.033 2.00e-02 2.50e+03 2.71e+00
  ... (remaining 2180 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 2891
        1.23 -     2.46: 80
        2.46 -     3.69: 15
        3.69 -     4.92: 6
        4.92 -     6.15: 4
  Bond angle restraints: 2996
  Sorted by residual:
  angle pdb=" C   VAL R  87 "
        pdb=" CA  VAL R  87 "
        pdb=" CB  VAL R  87 "
      ideal   model   delta    sigma   weight residual
     114.00  110.81    3.19 1.31e+00 5.83e-01 5.95e+00
  angle pdb=" C   VAL R  86 "
        pdb=" N   VAL R  87 "
        pdb=" CA  VAL R  87 "
      ideal   model   delta    sigma   weight residual
     120.33  122.16   -1.83 8.00e-01 1.56e+00 5.23e+00
  angle pdb=" CAG G1I R 501 "
        pdb=" CAH G1I R 501 "
        pdb=" CAI G1I R 501 "
      ideal   model   delta    sigma   weight residual
     110.89  117.04   -6.15 3.00e+00 1.11e-01 4.20e+00
  angle pdb=" N   CYS R 327 "
        pdb=" CA  CYS R 327 "
        pdb=" C   CYS R 327 "
      ideal   model   delta    sigma   weight residual
     110.06  112.70   -2.64 1.43e+00 4.89e-01 3.41e+00
  angle pdb=" N   LYS R 149 "
        pdb=" CA  LYS R 149 "
        pdb=" C   LYS R 149 "
      ideal   model   delta    sigma   weight residual
     113.50  111.33    2.17 1.23e+00 6.61e-01 3.11e+00
  ... (remaining 2991 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.75: 1090
       13.75 -    27.49: 117
       27.49 -    41.24: 34
       41.24 -    54.99: 4
       54.99 -    68.73: 1
  Dihedral angle restraints: 1246
    sinusoidal: 418
      harmonic: 828
  Sorted by residual:
  dihedral pdb=" CB  CYS R 106 "
           pdb=" SG  CYS R 106 "
           pdb=" SG  CYS R 191 "
           pdb=" CB  CYS R 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -154.73   68.73     1      1.00e+01 1.00e-02 6.12e+01
  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 -161.20  -18.80     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  HIS R 178 "
           pdb=" C   HIS R 178 "
           pdb=" N   GLN R 179 "
           pdb=" CA  GLN R 179 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.93  -17.07     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 1243 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 224
       0.031 -    0.061: 107
       0.061 -    0.092: 26
       0.092 -    0.122: 11
       0.122 -    0.153: 1
  Chirality restraints: 369
  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    2.55   -0.15 2.00e-01 2.50e+01 5.82e-01
  chirality pdb=" CA  TRP R 286 "
            pdb=" N   TRP R 286 "
            pdb=" C   TRP R 286 "
            pdb=" CB  TRP R 286 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.41    0.10 2.00e-01 2.50e+01 2.62e-01
  chirality pdb=" CA  PRO R 168 "
            pdb=" N   PRO R 168 "
            pdb=" C   PRO R 168 "
            pdb=" CB  PRO R 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.62    0.10 2.00e-01 2.50e+01 2.42e-01
  ... (remaining 366 not shown)

  Planarity restraints: 359
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 277 "   -0.007 2.00e-02 2.50e+03   1.30e-02 1.70e+00
        pdb=" C   ILE R 277 "    0.023 2.00e-02 2.50e+03
        pdb=" O   ILE R 277 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   ILE R 278 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 210 "    0.018 5.00e-02 4.00e+02   2.65e-02 1.12e+00
        pdb=" N   PRO R 211 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO R 211 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO R 211 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 322 "    0.017 5.00e-02 4.00e+02   2.50e-02 1.00e+00
        pdb=" N   PRO R 323 "   -0.043 5.00e-02 4.00e+02
        pdb=" CA  PRO R 323 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO R 323 "    0.014 5.00e-02 4.00e+02
  ... (remaining 356 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 651
        2.83 -     3.35: 2110
        3.35 -     3.87: 3364
        3.87 -     4.38: 3493
        4.38 -     4.90: 6394
  Nonbonded interactions: 16012
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAL G1I R 501 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" O   ALA R  92 "
            pdb=" OG1 THR R  96 "
     model   vdw
     2.484 3.040
  nonbonded pdb=" N   ASN R 196 "
            pdb=" OD1 ASN R 196 "
     model   vdw
     2.522 3.120
  nonbonded pdb=" OG  SER R 165 "
            pdb=" N   PHE R 166 "
     model   vdw
     2.539 3.120
  nonbonded pdb=" N   THR R  66 "
            pdb=" O   THR R  66 "
     model   vdw
     2.600 2.496
  ... (remaining 16007 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 individual isotropic
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:             1.420
  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:                    0.020
  Process input model:                     11.100
  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:2.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
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   0.053   2185  Z= 0.255
  Angle     :  0.551   6.147   2996  Z= 0.306
  Chirality :  0.038   0.153    369
  Planarity :  0.003   0.026    359
  Dihedral  : 12.049  54.423    705
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  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:  2.40 (0.50), residues: 277
  helix:  2.36 (0.36), residues: 203
  sheet:  None (None), residues: 0
  loop : -0.64 (0.70), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 109 
 HIS   0.007   0.002   HIS R 296 
 PHE   0.012   0.001   PHE R 282 
 TYR   0.009   0.001   TYR R 219 
 ARG   0.002   0.000   ARG R 239 

*********************** 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
  22 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.218 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.2386
  time to fit residues: 6.0142
Evaluate side-chains
  18 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   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 = 0.3440 r_free = 0.3440 target = 0.130095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.115334 restraints weight = 2912.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 1.61
r_work: 0.3175 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.0796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2185  Z= 0.217
  Angle     :  0.488   5.636   2996  Z= 0.279
  Chirality :  0.039   0.127    369
  Planarity :  0.003   0.028    359
  Dihedral  :  4.447  18.466    313
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  6.25 %
    Favored  : 93.27 %
  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:  2.63 (0.52), residues: 277
  helix:  2.45 (0.35), residues: 217
  sheet:  None (None), residues: 0
  loop : -1.01 (0.80), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.004   0.002   HIS R 296 
 PHE   0.013   0.001   PHE R 282 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.002   0.000   ARG R 239 

*********************** 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
  23 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.230 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 22
  average time/residue: 0.1728
  time to fit residues: 4.6005
Evaluate side-chains
  21 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.129200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.113261 restraints weight = 2915.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 1.69
r_work: 0.3161 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2185  Z= 0.229
  Angle     :  0.481   5.283   2996  Z= 0.275
  Chirality :  0.039   0.125    369
  Planarity :  0.003   0.027    359
  Dihedral  :  4.400  19.790    313
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 11.54 %
    Favored  : 87.02 %
  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:  2.72 (0.52), residues: 277
  helix:  2.46 (0.35), residues: 218
  sheet:  None (None), residues: 0
  loop : -0.84 (0.83), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.002   0.001   HIS R  93 
 PHE   0.013   0.001   PHE R 282 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.002   0.000   ARG R 239 

*********************** 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
  24 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.207 
Fit side-chains
REVERT: R   63 ARG cc_start: 0.4168 (mmt90) cc_final: 0.1881 (ttm170)
  outliers start: 3
  outliers final: 2
  residues processed: 23
  average time/residue: 0.1669
  time to fit residues: 4.5930
Evaluate side-chains
  23 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 21
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 26 optimal weight:    0.4980
   chunk 4 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0020
   chunk 14 optimal weight:    0.0020
   chunk 10 optimal weight:    0.6980
   chunk 16 optimal weight:    0.1980
   chunk 13 optimal weight:    0.0570
   overall best weight:    0.1514

-------------------------------------------------------------------------------
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 = 0.3537 r_free = 0.3537 target = 0.138663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.123692 restraints weight = 2772.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 1.56
r_work: 0.3311 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3202
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3202
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.1357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   2185  Z= 0.126
  Angle     :  0.411   4.829   2996  Z= 0.230
  Chirality :  0.037   0.112    369
  Planarity :  0.003   0.026    359
  Dihedral  :  3.995  18.602    313
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 12.50 %
    Favored  : 86.06 %
  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:  3.12 (0.52), residues: 277
  helix:  2.66 (0.35), residues: 223
  sheet:  None (None), residues: 0
  loop : -0.63 (0.89), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 313 
 HIS   0.002   0.000   HIS R 178 
 PHE   0.009   0.001   PHE R 282 
 TYR   0.006   0.001   TYR R 209 
 ARG   0.001   0.000   ARG R 175 

*********************** 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
  28 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.220 
Fit side-chains
REVERT: R   72 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.8024 (mt)
  outliers start: 3
  outliers final: 1
  residues processed: 27
  average time/residue: 0.1393
  time to fit residues: 4.5938
Evaluate side-chains
  24 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 18 optimal weight:    0.4980
   chunk 11 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 27 optimal weight:    0.2980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3462 r_free = 0.3462 target = 0.131963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.116103 restraints weight = 2879.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 1.64
r_work: 0.3247 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3137 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3084
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3084
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.1260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2185  Z= 0.192
  Angle     :  0.441   4.932   2996  Z= 0.251
  Chirality :  0.038   0.118    369
  Planarity :  0.003   0.024    359
  Dihedral  :  4.038  18.123    313
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 1.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 16.35 %
    Favored  : 82.21 %
  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:  3.09 (0.52), residues: 277
  helix:  2.63 (0.35), residues: 224
  sheet:  None (None), residues: 0
  loop : -0.62 (0.87), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.013   0.001   PHE R 282 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.002   0.000   ARG R 239 

*********************** 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
  24 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.240 
Fit side-chains
REVERT: R   63 ARG cc_start: 0.4341 (mmt90) cc_final: 0.1966 (ttm170)
REVERT: R   72 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8183 (mt)
  outliers start: 3
  outliers final: 2
  residues processed: 24
  average time/residue: 0.1621
  time to fit residues: 4.7135
Evaluate side-chains
  24 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 3 optimal weight:    0.0980
   chunk 5 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 21 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 = 0.3432 r_free = 0.3432 target = 0.129539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.113656 restraints weight = 2874.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 1.64
r_work: 0.3170 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3095
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3095 r_free = 0.3095    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3095 r_free = 0.3095    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3095
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.1275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2185  Z= 0.221
  Angle     :  0.456   4.988   2996  Z= 0.262
  Chirality :  0.039   0.123    369
  Planarity :  0.003   0.025    359
  Dihedral  :  4.183  18.476    313
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 17.79 %
    Favored  : 80.29 %
  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:  2.94 (0.52), residues: 277
  helix:  2.70 (0.35), residues: 217
  sheet:  None (None), residues: 0
  loop : -1.03 (0.80), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.013   0.001   PHE R 282 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.002   0.000   ARG R 239 

*********************** 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
  26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 22
  time to evaluate  : 0.237 
Fit side-chains
REVERT: R   63 ARG cc_start: 0.4434 (mmt90) cc_final: 0.2043 (ttm170)
REVERT: R   72 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8088 (mt)
  outliers start: 4
  outliers final: 3
  residues processed: 26
  average time/residue: 0.1592
  time to fit residues: 5.0143
Evaluate side-chains
  25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  218 VAL
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 19 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0170
   chunk 20 optimal weight:    0.4980
   chunk 9 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.4818

-------------------------------------------------------------------------------
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 = 0.3453 r_free = 0.3453 target = 0.131446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.116096 restraints weight = 2945.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 1.64
r_work: 0.3197 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3089 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3080
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3080
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.1347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2185  Z= 0.177
  Angle     :  0.432   4.935   2996  Z= 0.247
  Chirality :  0.038   0.120    369
  Planarity :  0.003   0.025    359
  Dihedral  :  4.084  18.579    313
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 17.79 %
    Favored  : 79.81 %
  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:  3.01 (0.52), residues: 277
  helix:  2.75 (0.35), residues: 217
  sheet:  None (None), residues: 0
  loop : -1.04 (0.80), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.002   0.001   HIS R 178 
 PHE   0.011   0.001   PHE R 282 
 TYR   0.006   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R 239 

*********************** 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
  26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.240 
Fit side-chains
REVERT: R   63 ARG cc_start: 0.4325 (mmt90) cc_final: 0.2060 (ttm170)
REVERT: R   72 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8085 (mt)
  outliers start: 5
  outliers final: 4
  residues processed: 26
  average time/residue: 0.1704
  time to fit residues: 5.4106
Evaluate side-chains
  26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0870
   chunk 20 optimal weight:    0.7980
   chunk 5 optimal weight:    0.1980
   chunk 17 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0970
   chunk 9 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0050
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.1970

-------------------------------------------------------------------------------
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 = 0.3529 r_free = 0.3529 target = 0.137900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.121695 restraints weight = 2869.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 1.69
r_work: 0.3269 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3148
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3148
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.1600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   2185  Z= 0.125
  Angle     :  0.399   4.916   2996  Z= 0.224
  Chirality :  0.037   0.111    369
  Planarity :  0.003   0.025    359
  Dihedral  :  3.844  18.632    313
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 1.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 18.27 %
    Favored  : 79.81 %
  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:  3.32 (0.52), residues: 277
  helix:  2.82 (0.34), residues: 223
  sheet:  None (None), residues: 0
  loop : -0.65 (0.87), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 313 
 HIS   0.001   0.000   HIS R 296 
 PHE   0.010   0.001   PHE R 282 
 TYR   0.006   0.001   TYR R 209 
 ARG   0.001   0.000   ARG R 131 

*********************** 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
  29 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 25
  time to evaluate  : 0.259 
Fit side-chains
REVERT: R   63 ARG cc_start: 0.4144 (mmt90) cc_final: 0.2280 (ttm170)
REVERT: R   72 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8032 (mt)
  outliers start: 4
  outliers final: 3
  residues processed: 29
  average time/residue: 0.1529
  time to fit residues: 5.4700
Evaluate side-chains
  28 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 16 optimal weight:    0.4980
   chunk 9 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0060
   chunk 17 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.4996

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.132534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.117307 restraints weight = 2938.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 1.60
r_work: 0.3278 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3112
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3112 r_free = 0.3112    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3112 r_free = 0.3112    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3112
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.1496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2185  Z= 0.184
  Angle     :  0.435   4.976   2996  Z= 0.250
  Chirality :  0.038   0.116    369
  Planarity :  0.003   0.024    359
  Dihedral  :  3.922  18.272    313
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 18.27 %
    Favored  : 79.81 %
  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:  3.35 (0.52), residues: 277
  helix:  2.79 (0.34), residues: 223
  sheet:  None (None), residues: 0
  loop : -0.38 (0.96), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.012   0.001   PHE R 282 
 TYR   0.006   0.001   TYR R 199 
 ARG   0.002   0.000   ARG R 239 

*********************** 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
  26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 22
  time to evaluate  : 0.229 
Fit side-chains
REVERT: R   63 ARG cc_start: 0.4475 (mmt90) cc_final: 0.2144 (ttm170)
REVERT: R   72 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8176 (mt)
  outliers start: 4
  outliers final: 3
  residues processed: 26
  average time/residue: 0.1521
  time to fit residues: 4.8532
Evaluate side-chains
  25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue  143 SER
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 24 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 26 optimal weight:    0.2980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3446 r_free = 0.3446 target = 0.130737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.115445 restraints weight = 2930.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 1.59
r_work: 0.3186 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3080
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3080
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2185  Z= 0.211
  Angle     :  0.451   5.014   2996  Z= 0.259
  Chirality :  0.038   0.118    369
  Planarity :  0.003   0.024    359
  Dihedral  :  4.035  18.422    313
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 18.75 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.15 (0.52), residues: 277
  helix:  2.72 (0.35), residues: 224
  sheet:  None (None), residues: 0
  loop : -0.87 (0.87), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.012   0.001   PHE R 282 
 TYR   0.006   0.001   TYR R 199 
 ARG   0.002   0.000   ARG R 239 

********************** 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
  26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 22
  time to evaluate  : 0.195 
Fit side-chains
REVERT: R   63 ARG cc_start: 0.4295 (mmt90) cc_final: 0.2112 (ttm170)
REVERT: R   72 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8066 (mt)
  outliers start: 4
  outliers final: 3
  residues processed: 26
  average time/residue: 0.1494
  time to fit residues: 4.6861
Evaluate side-chains
  26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 22
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue  143 SER
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 10 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0370
   chunk 22 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0470
   chunk 11 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.3756

-------------------------------------------------------------------------------
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 = 0.3479 r_free = 0.3479 target = 0.133588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.117251 restraints weight = 2852.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 1.69
r_work: 0.3217 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3104 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3135
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3135
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   2185  Z= 0.162
  Angle     :  0.424   4.920   2996  Z= 0.243
  Chirality :  0.037   0.115    369
  Planarity :  0.003   0.024    359
  Dihedral  :  3.956  18.531    313
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 18.27 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.20 (0.52), residues: 277
  helix:  2.78 (0.35), residues: 224
  sheet:  None (None), residues: 0
  loop : -1.01 (0.86), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.011   0.001   PHE R 282 
 TYR   0.006   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R 239 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1532.12 seconds
wall clock time: 27 minutes 46.62 seconds (1666.62 seconds total)