Starting phenix.real_space_refine
on Sat Apr 26 15:45:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggq_40017/04_2025/8ggq_40017.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggq_40017/04_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_40017/04_2025/8ggq_40017.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggq_40017/04_2025/8ggq_40017.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggq_40017/04_2025/8ggq_40017.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggq_40017/04_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-5669/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: 4.53, per 1000 atoms: 2.13
  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: 0.65
  Conformation dependent library (CDL) restraints added in 345.4 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: 0.22
  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: 0.61

  Time building geometry restraints manager: 0.78 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:             3.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     14.570
  Find NCS groups from input model:        0.030
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.910
-------------------------------------------------------------------------------
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   2186  Z= 0.191
  Angle     :  0.551   6.147   2998  Z= 0.307
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15540 (  166)
  hydrogen bonds       : angle       5.17061 (  498)
  SS BOND              : bond        0.00011 (    1)
  SS BOND              : angle       1.08636 (    2)
  covalent geometry    : bond        0.00377 ( 2185)
  covalent geometry    : angle       0.55090 ( 2996)

*********************** 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  : 0.233 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.2498
  time to fit residues: 6.3202
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  : 0.234 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3427 r_free = 0.3427 target = 0.128998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.114160 restraints weight = 2925.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 1.62
r_work: 0.3188 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3054
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3055 r_free = 0.3055    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3055
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.0805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   2186  Z= 0.162
  Angle     :  0.500   5.910   2998  Z= 0.287
  Chirality :  0.039   0.128    369
  Planarity :  0.003   0.028    359
  Dihedral  :  4.486  18.459    313
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  6.73 %
    Favored  : 92.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.59 (0.51), residues: 277
  helix:  2.42 (0.35), residues: 217
  sheet:  None (None), residues: 0
  loop : -1.03 (0.79), 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   0.008   0.001   TYR R 199 
 ARG   0.003   0.000   ARG R 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06871 (  166)
  hydrogen bonds       : angle       4.29898 (  498)
  SS BOND              : bond        0.00350 (    1)
  SS BOND              : angle       1.03588 (    2)
  covalent geometry    : bond        0.00356 ( 2185)
  covalent geometry    : angle       0.49984 ( 2996)

*********************** 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  : 0.244 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 22
  average time/residue: 0.1731
  time to fit residues: 4.6000
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  : 0.255 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0040
   chunk 14 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0010
   chunk 2 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0980
   overall best weight:    0.2798

-------------------------------------------------------------------------------
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 = 0.3618 r_free = 0.3618 target = 0.145570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.130980 restraints weight = 2819.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.55
r_work: 0.3290 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3139
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3139 r_free = 0.3139    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3140
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.1128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   2186  Z= 0.111
  Angle     :  0.427   4.926   2998  Z= 0.240
  Chirality :  0.037   0.119    369
  Planarity :  0.003   0.025    359
  Dihedral  :  4.127  19.022    313
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  9.62 %
    Favored  : 88.94 %
  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:  2.95 (0.52), residues: 277
  helix:  2.56 (0.35), residues: 223
  sheet:  None (None), residues: 0
  loop : -0.75 (0.86), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.001   0.000   HIS R 178 
 PHE   0.010   0.001   PHE R 282 
 TYR   0.006   0.001   TYR R 209 
 ARG   0.001   0.000   ARG R 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05121 (  166)
  hydrogen bonds       : angle       3.92196 (  498)
  SS BOND              : bond        0.00009 (    1)
  SS BOND              : angle       0.71797 (    2)
  covalent geometry    : bond        0.00212 ( 2185)
  covalent geometry    : angle       0.42672 ( 2996)

*********************** 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
  26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 23
  time to evaluate  : 0.229 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 25
  average time/residue: 0.1352
  time to fit residues: 4.1127
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  : 0.213 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0020
   overall best weight:    0.6388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.130272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.114388 restraints weight = 2889.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 1.65
r_work: 0.3172 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3060 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3062
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    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 = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3062
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.1119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2186  Z= 0.148
  Angle     :  0.460   4.971   2998  Z= 0.263
  Chirality :  0.039   0.122    369
  Planarity :  0.003   0.025    359
  Dihedral  :  4.187  18.135    313
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 12.98 %
    Favored  : 84.62 %
  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:  3.02 (0.52), residues: 277
  helix:  2.65 (0.35), residues: 219
  sheet:  None (None), residues: 0
  loop : -0.70 (0.84), residues: 58

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   0.013   0.001   PHE R 282 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.003   0.000   ARG R 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06271 (  166)
  hydrogen bonds       : angle       4.03212 (  498)
  SS BOND              : bond        0.00250 (    1)
  SS BOND              : angle       0.80251 (    2)
  covalent geometry    : bond        0.00324 ( 2185)
  covalent geometry    : angle       0.46015 ( 2996)

*********************** 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
  26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.250 
Fit side-chains
REVERT: R   63 ARG cc_start: 0.4102 (mmt90) cc_final: 0.1911 (ttm170)
REVERT: R   72 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8041 (mt)
  outliers start: 5
  outliers final: 3
  residues processed: 25
  average time/residue: 0.1638
  time to fit residues: 4.9612
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  : 0.185 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 10 optimal weight:    0.3980
   chunk 23 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0970
   chunk 11 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.3578

-------------------------------------------------------------------------------
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 = 0.3481 r_free = 0.3481 target = 0.133910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.118578 restraints weight = 2852.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 1.61
r_work: 0.3290 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3111
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3111 r_free = 0.3111    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 = 0.3111 r_free = 0.3111    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3111
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.1243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   2186  Z= 0.114
  Angle     :  0.417   4.894   2998  Z= 0.237
  Chirality :  0.037   0.118    369
  Planarity :  0.003   0.025    359
  Dihedral  :  4.019  18.509    313
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 1.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 14.90 %
    Favored  : 83.65 %
  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:  3.14 (0.52), residues: 277
  helix:  2.81 (0.35), residues: 217
  sheet:  None (None), residues: 0
  loop : -0.82 (0.82), 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 178 
 PHE   0.010   0.001   PHE R 282 
 TYR   0.006   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05323 (  166)
  hydrogen bonds       : angle       3.88006 (  498)
  SS BOND              : bond        0.00092 (    1)
  SS BOND              : angle       0.61968 (    2)
  covalent geometry    : bond        0.00225 ( 2185)
  covalent geometry    : angle       0.41697 ( 2996)

*********************** 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  : 0.251 
Fit side-chains
REVERT: R   63 ARG cc_start: 0.4085 (mmt90) cc_final: 0.2199 (ttm170)
REVERT: R   72 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8067 (mt)
  outliers start: 3
  outliers final: 2
  residues processed: 24
  average time/residue: 0.1812
  time to fit residues: 5.2689
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:    0.5980
   chunk 5 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 23 optimal weight:    0.3980
   chunk 21 optimal weight:    0.6980
   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 = 0.3445 r_free = 0.3445 target = 0.130730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.115691 restraints weight = 2855.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 1.57
r_work: 0.3243 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3135 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3083
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    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 = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3083
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.1244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2186  Z= 0.143
  Angle     :  0.445   4.959   2998  Z= 0.255
  Chirality :  0.038   0.120    369
  Planarity :  0.003   0.024    359
  Dihedral  :  4.098  18.231    313
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 1.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.35 %
    Favored  : 81.73 %
  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:  3.07 (0.52), residues: 277
  helix:  2.75 (0.35), residues: 218
  sheet:  None (None), residues: 0
  loop : -0.85 (0.82), 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 296 
 PHE   0.013   0.001   PHE R 282 
 TYR   0.006   0.001   TYR R 199 
 ARG   0.002   0.000   ARG R 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06110 (  166)
  hydrogen bonds       : angle       3.97258 (  498)
  SS BOND              : bond        0.00294 (    1)
  SS BOND              : angle       0.70225 (    2)
  covalent geometry    : bond        0.00316 ( 2185)
  covalent geometry    : angle       0.44501 ( 2996)

*********************** 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  : 0.241 
Fit side-chains
REVERT: R   63 ARG cc_start: 0.4463 (mmt90) cc_final: 0.2130 (ttm170)
REVERT: R   72 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8177 (mt)
  outliers start: 4
  outliers final: 3
  residues processed: 26
  average time/residue: 0.1537
  time to fit residues: 4.8566
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  : 0.239 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0770
   overall best weight:    0.5738

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.130934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.115769 restraints weight = 2958.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 1.59
r_work: 0.3192 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    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 = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.1304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2186  Z= 0.137
  Angle     :  0.442   4.985   2998  Z= 0.253
  Chirality :  0.038   0.121    369
  Planarity :  0.003   0.025    359
  Dihedral  :  4.119  18.527    313
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 2.16
  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:  3.02 (0.52), residues: 277
  helix:  2.73 (0.35), residues: 218
  sheet:  None (None), residues: 0
  loop : -0.97 (0.82), 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 178 
 PHE   0.012   0.001   PHE R 282 
 TYR   0.006   0.001   TYR R 199 
 ARG   0.002   0.000   ARG R 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06050 (  166)
  hydrogen bonds       : angle       3.97711 (  498)
  SS BOND              : bond        0.00266 (    1)
  SS BOND              : angle       0.67053 (    2)
  covalent geometry    : bond        0.00295 ( 2185)
  covalent geometry    : angle       0.44168 ( 2996)

*********************** 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  : 0.254 
Fit side-chains
REVERT: R   63 ARG cc_start: 0.4392 (mmt90) cc_final: 0.2026 (ttm170)
REVERT: R   72 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8102 (mt)
  outliers start: 5
  outliers final: 4
  residues processed: 26
  average time/residue: 0.1598
  time to fit residues: 5.0485
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  : 0.234 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 15 optimal weight:    0.1980
   chunk 11 optimal weight:    0.0980
   chunk 20 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0060
   chunk 17 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 10 optimal weight:    0.2980
   chunk 9 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.2396

-------------------------------------------------------------------------------
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 = 0.3511 r_free = 0.3511 target = 0.136406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.121029 restraints weight = 2893.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 1.63
r_work: 0.3256 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3144
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3144 r_free = 0.3144    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 = 0.3144 r_free = 0.3144    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3144
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.1524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   2186  Z= 0.101
  Angle     :  0.402   4.911   2998  Z= 0.226
  Chirality :  0.037   0.113    369
  Planarity :  0.003   0.025    359
  Dihedral  :  3.878  18.610    313
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 1.92
  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:  3.31 (0.52), residues: 277
  helix:  2.83 (0.35), residues: 223
  sheet:  None (None), residues: 0
  loop : -0.74 (0.87), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.001   0.000   HIS R 178 
 PHE   0.010   0.001   PHE R 282 
 TYR   0.006   0.001   TYR R 209 
 ARG   0.001   0.000   ARG R 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04635 (  166)
  hydrogen bonds       : angle       3.72340 (  498)
  SS BOND              : bond        0.00032 (    1)
  SS BOND              : angle       0.52266 (    2)
  covalent geometry    : bond        0.00188 ( 2185)
  covalent geometry    : angle       0.40168 ( 2996)

*********************** 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
  30 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.273 
Fit side-chains
REVERT: R   63 ARG cc_start: 0.4054 (mmt90) cc_final: 0.2301 (ttm170)
REVERT: R   72 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8027 (mt)
  outliers start: 4
  outliers final: 3
  residues processed: 29
  average time/residue: 0.1379
  time to fit residues: 4.9433
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  : 0.241 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 6 optimal weight:    0.0370
   chunk 12 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0980
   chunk 17 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.4058

-------------------------------------------------------------------------------
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 = 0.3485 r_free = 0.3485 target = 0.134061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.117882 restraints weight = 2906.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 1.69
r_work: 0.3234 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
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: 0.8063
moved from start:          0.1525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   2186  Z= 0.115
  Angle     :  0.415   4.963   2998  Z= 0.235
  Chirality :  0.037   0.113    369
  Planarity :  0.003   0.024    359
  Dihedral  :  3.877  18.390    313
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 2.16
  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:  3.33 (0.52), residues: 277
  helix:  2.85 (0.34), residues: 223
  sheet:  None (None), residues: 0
  loop : -0.76 (0.88), 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   0.011   0.001   PHE R 282 
 TYR   0.006   0.001   TYR R 209 
 ARG   0.001   0.000   ARG R 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05091 (  166)
  hydrogen bonds       : angle       3.77109 (  498)
  SS BOND              : bond        0.00115 (    1)
  SS BOND              : angle       0.63949 (    2)
  covalent geometry    : bond        0.00237 ( 2185)
  covalent geometry    : angle       0.41459 ( 2996)

*********************** 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
  27 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.218 
Fit side-chains
REVERT: R   63 ARG cc_start: 0.4266 (mmt90) cc_final: 0.2011 (ttm170)
REVERT: R   72 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8062 (mt)
  outliers start: 4
  outliers final: 3
  residues processed: 27
  average time/residue: 0.1500
  time to fit residues: 4.8853
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  : 0.218 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 25 optimal weight:    0.2980
   chunk 20 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   chunk 5 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.132145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.116067 restraints weight = 2901.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 1.65
r_work: 0.3195 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
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: 0.8073
moved from start:          0.1492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2186  Z= 0.131
  Angle     :  0.435   4.958   2998  Z= 0.249
  Chirality :  0.038   0.115    369
  Planarity :  0.003   0.024    359
  Dihedral  :  3.968  18.321    313
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  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:  3.16 (0.51), residues: 277
  helix:  2.78 (0.35), residues: 224
  sheet:  None (None), residues: 0
  loop : -1.15 (0.81), 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   0.013   0.001   PHE R 290 
 TYR   0.006   0.001   TYR R 199 
 ARG   0.002   0.000   ARG R 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05667 (  166)
  hydrogen bonds       : angle       3.85370 (  498)
  SS BOND              : bond        0.00233 (    1)
  SS BOND              : angle       0.72965 (    2)
  covalent geometry    : bond        0.00282 ( 2185)
  covalent geometry    : angle       0.43426 ( 2996)

********************** 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
  28 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 23
  time to evaluate  : 0.225 
Fit side-chains
REVERT: R   63 ARG cc_start: 0.4289 (mmt90) cc_final: 0.1998 (ttm170)
REVERT: R   72 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8045 (mt)
  outliers start: 5
  outliers final: 4
  residues processed: 27
  average time/residue: 0.1506
  time to fit residues: 4.9216
Evaluate side-chains
  28 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 23
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   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 = 0.3428 r_free = 0.3428 target = 0.129359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.113323 restraints weight = 2898.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 1.63
r_work: 0.3162 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3045
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3045
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2186  Z= 0.151
  Angle     :  0.460   5.020   2998  Z= 0.265
  Chirality :  0.039   0.122    369
  Planarity :  0.003   0.024    359
  Dihedral  :  4.159  18.302    313
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 18.27 %
    Favored  : 78.85 %
  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:  2.92 (0.52), residues: 277
  helix:  2.74 (0.35), residues: 219
  sheet:  None (None), residues: 0
  loop : -1.45 (0.77), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.003   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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06432 (  166)
  hydrogen bonds       : angle       4.00852 (  498)
  SS BOND              : bond        0.00377 (    1)
  SS BOND              : angle       0.78385 (    2)
  covalent geometry    : bond        0.00337 ( 2185)
  covalent geometry    : angle       0.45973 ( 2996)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1671.87 seconds
wall clock time: 29 minutes 17.62 seconds (1757.62 seconds total)