Starting phenix.real_space_refine
on Fri May  9 13:22:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggt_40020/05_2025/8ggt_40020.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggt_40020/05_2025/8ggt_40020.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ggt_40020/05_2025/8ggt_40020.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggt_40020/05_2025/8ggt_40020.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggt_40020/05_2025/8ggt_40020.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggt_40020/05_2025/8ggt_40020.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    1405      2.51       5
     N     335      2.21       5
     O     350      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-5687/modules/chem_data/mon_lib"
  Total number of atoms: 2105
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2090
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2090
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 174
          Unresolved non-hydrogen angles: 218
          Unresolved non-hydrogen dihedrals: 146
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 95
    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: 2.38, per 1000 atoms: 1.13
  Number of scatterers: 2105
  At special positions: 0
  Unit cell: (56.4005, 84.1669, 61.6067, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      15     16.00
     O     350      8.00
     N     335      7.00
     C    1405      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: 0.57
  Conformation dependent library (CDL) restraints added in 268.3 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:
      12 helices and 0 sheets defined
      86.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'R' and resid 37 through 61
      removed outlier: 3.787A  pdb=" N   ILE R  43 " --> pdb=" O   VAL R  39 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   VAL R  44 " --> pdb=" O   MET R  40 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 96
      removed outlier: 3.580A  pdb=" N   TYR R  70 " --> pdb=" O   THR R  66 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 5.254A  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: 3.739A  pdb=" N   CYS R 106 " --> pdb=" O   GLY R 102 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
      removed outlier: 3.722A  pdb=" N   LEU R 144 " --> pdb=" O   LYS R 140 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU R 145 " --> pdb=" O   TYR R 141 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 140 through 145'
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.595A  pdb=" N   ALA R 150 " --> pdb=" O   THR R 146 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   SER R 165 " --> pdb=" O   SER R 161 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 237
      removed outlier: 3.835A  pdb=" N   SER R 236 " --> pdb=" O   LYS R 232 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 299
      removed outlier: 3.842A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.674A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ILE R 298 " --> pdb=" O   ILE R 294 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.554A  pdb=" N   TYR R 308 " --> pdb=" O   ARG R 304 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 317 through 327
      removed outlier: 3.715A  pdb=" N   PHE R 321 " --> pdb=" O   VAL R 317 " (cutoff:3.500A)
      removed outlier: 3.544A  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

    160 hydrogen bonds defined for protein.
    480 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.51

  Time building geometry restraints manager: 0.66 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 385
        1.33 -     1.45: 561
        1.45 -     1.57: 1190
        1.57 -     1.69: 1
        1.69 -     1.81: 22
  Bond restraints: 2159
  Sorted by residual:
  bond pdb=" C   LEU R 287 "
       pdb=" O   LEU R 287 "
    ideal  model  delta    sigma   weight residual
    1.244  1.211  0.032 9.80e-03 1.04e+04 1.09e+01
  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 7.10e+00
  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 6.91e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.567 -0.047 2.00e-02 2.50e+03 5.45e+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 5.28e+00
  ... (remaining 2154 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 2914
        2.19 -     4.39: 34
        4.39 -     6.58: 8
        6.58 -     8.77: 4
        8.77 -    10.96: 1
  Bond angle restraints: 2961
  Sorted by residual:
  angle pdb=" N   PHE R 289 "
        pdb=" CA  PHE R 289 "
        pdb=" C   PHE R 289 "
      ideal   model   delta    sigma   weight residual
     111.07  118.45   -7.38 1.07e+00 8.73e-01 4.75e+01
  angle pdb=" N   TRP R 286 "
        pdb=" CA  TRP R 286 "
        pdb=" C   TRP R 286 "
      ideal   model   delta    sigma   weight residual
     113.97  121.51   -7.54 1.28e+00 6.10e-01 3.47e+01
  angle pdb=" CA  MET R  36 "
        pdb=" CB  MET R  36 "
        pdb=" CG  MET R  36 "
      ideal   model   delta    sigma   weight residual
     114.10  121.69   -7.59 2.00e+00 2.50e-01 1.44e+01
  angle pdb=" CB  MET R  36 "
        pdb=" CG  MET R  36 "
        pdb=" SD  MET R  36 "
      ideal   model   delta    sigma   weight residual
     112.70  123.66  -10.96 3.00e+00 1.11e-01 1.34e+01
  angle pdb=" C   LEU R 287 "
        pdb=" N   PRO R 288 "
        pdb=" CA  PRO R 288 "
      ideal   model   delta    sigma   weight residual
     119.05  115.01    4.04 1.11e+00 8.12e-01 1.32e+01
  ... (remaining 2956 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.67: 1124
       16.67 -    33.33: 81
       33.33 -    49.99: 25
       49.99 -    66.66: 2
       66.66 -    83.32: 3
  Dihedral angle restraints: 1235
    sinusoidal: 407
      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 -169.32   83.32     1      1.00e+01 1.00e-02 8.48e+01
  dihedral pdb=" CA  LEU R 302 "
           pdb=" C   LEU R 302 "
           pdb=" N   ILE R 303 "
           pdb=" CA  ILE R 303 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.34  -18.66     0      5.00e+00 4.00e-02 1.39e+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 -161.81  -18.19     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 1232 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 254
       0.042 -    0.083: 90
       0.083 -    0.124: 18
       0.124 -    0.165: 0
       0.165 -    0.207: 2
  Chirality restraints: 364
  Sorted by residual:
  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    2.30    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.57   -0.17 2.00e-01 2.50e+01 7.05e-01
  chirality pdb=" CA  PHE R 289 "
            pdb=" N   PHE R 289 "
            pdb=" C   PHE R 289 "
            pdb=" CB  PHE R 289 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.61e-01
  ... (remaining 361 not shown)

  Planarity restraints: 358
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET R  36 "   -0.010 2.00e-02 2.50e+03   2.01e-02 4.03e+00
        pdb=" C   MET R  36 "    0.035 2.00e-02 2.50e+03
        pdb=" O   MET R  36 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLY R  37 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 287 "   -0.026 5.00e-02 4.00e+02   3.89e-02 2.42e+00
        pdb=" N   PRO R 288 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO R 288 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO R 288 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 281 "   -0.007 2.00e-02 2.50e+03   1.48e-02 2.19e+00
        pdb=" C   THR R 281 "    0.026 2.00e-02 2.50e+03
        pdb=" O   THR R 281 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   PHE R 282 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 355 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 408
        2.77 -     3.30: 2079
        3.30 -     3.84: 3341
        3.84 -     4.37: 3350
        4.37 -     4.90: 6282
  Nonbonded interactions: 15460
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAL G1I R 501 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OD2 ASP R 113 "
            pdb=" OH  TYR R 316 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" NE1 TRP R  99 "
            pdb=" O   GLY R 102 "
     model   vdw
     2.504 3.120
  nonbonded pdb=" OH  TYR R 185 "
            pdb=" O   PHE R 194 "
     model   vdw
     2.527 3.040
  nonbonded pdb=" OG  SER R 165 "
            pdb=" N   PHE R 166 "
     model   vdw
     2.531 3.120
  ... (remaining 15455 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.580
  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:          0.060
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     10.520
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
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   2160  Z= 0.252
  Angle     :  0.700  10.965   2963  Z= 0.420
  Chirality :  0.041   0.207    364
  Planarity :  0.004   0.039    358
  Dihedral  : 13.407  78.387    694
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.49), residues: 277
  helix:  2.41 (0.35), residues: 206
  sheet:  None (None), residues: 0
  loop : -2.50 (0.55), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R 178 
 PHE   0.012   0.001   PHE R 139 
 TYR   0.009   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14554 (  160)
  hydrogen bonds       : angle       4.98303 (  480)
  SS BOND              : bond        0.00106 (    1)
  SS BOND              : angle       0.23885 (    2)
  covalent geometry    : bond        0.00447 ( 2159)
  covalent geometry    : angle       0.70009 ( 2961)

*********************** 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
  21 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.1535
  time to fit residues: 3.9793
Evaluate side-chains
  16 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0050
   chunk 7 optimal weight:    0.0870
   chunk 14 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.4172

-------------------------------------------------------------------------------
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 = 0.3639 r_free = 0.3639 target = 0.146538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.131920 restraints weight = 3009.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.134606 restraints weight = 1621.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.136512 restraints weight = 1054.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.0730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2160  Z= 0.132
  Angle     :  0.490   6.438   2963  Z= 0.277
  Chirality :  0.039   0.156    364
  Planarity :  0.004   0.032    358
  Dihedral  :  4.430  17.988    311
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  5.50 %
    Favored  : 92.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.50), residues: 277
  helix:  2.64 (0.35), residues: 209
  sheet:  None (None), residues: 0
  loop : -2.42 (0.62), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 286 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.010   0.001   PHE R 139 
 TYR   0.008   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06063 (  160)
  hydrogen bonds       : angle       4.00623 (  480)
  SS BOND              : bond        0.00052 (    1)
  SS BOND              : angle       0.22712 (    2)
  covalent geometry    : bond        0.00260 ( 2159)
  covalent geometry    : angle       0.48994 ( 2961)

*********************** 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
  21 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 17
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7396 (mtt) cc_final: 0.7114 (mtt)
  outliers start: 4
  outliers final: 4
  residues processed: 19
  average time/residue: 0.1317
  time to fit residues: 3.2065
Evaluate side-chains
  20 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 16
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  182 ILE
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  309 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0020
   chunk 13 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.5788

-------------------------------------------------------------------------------
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 = 0.3645 r_free = 0.3645 target = 0.147053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.132291 restraints weight = 3035.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.134858 restraints weight = 1694.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.136851 restraints weight = 1130.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.1026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2160  Z= 0.139
  Angle     :  0.493   6.127   2963  Z= 0.275
  Chirality :  0.039   0.131    364
  Planarity :  0.004   0.025    358
  Dihedral  :  4.420  17.810    311
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  7.00 %
    Favored  : 91.00 %
  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:  2.33 (0.51), residues: 277
  helix:  2.71 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.39 (0.66), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 286 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.015   0.001   PHE R 139 
 TYR   0.009   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06086 (  160)
  hydrogen bonds       : angle       3.89764 (  480)
  SS BOND              : bond        0.00004 (    1)
  SS BOND              : angle       0.30585 (    2)
  covalent geometry    : bond        0.00289 ( 2159)
  covalent geometry    : angle       0.49274 ( 2961)

*********************** 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
  21 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 17
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7537 (mtt) cc_final: 0.7241 (mtt)
  outliers start: 4
  outliers final: 4
  residues processed: 19
  average time/residue: 0.0857
  time to fit residues: 2.3782
Evaluate side-chains
  20 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 16
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  182 ILE
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 7 optimal weight:    0.4980
   chunk 5 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0670
   chunk 26 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.6118

-------------------------------------------------------------------------------
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 = 0.3638 r_free = 0.3638 target = 0.146281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.131536 restraints weight = 3069.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.134085 restraints weight = 1732.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.135999 restraints weight = 1160.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.1110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2160  Z= 0.140
  Angle     :  0.494   7.005   2963  Z= 0.275
  Chirality :  0.039   0.130    364
  Planarity :  0.004   0.026    358
  Dihedral  :  4.377  17.719    311
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 1.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  :  8.50 %
    Favored  : 88.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.33 (0.52), residues: 277
  helix:  2.69 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.35 (0.69), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 286 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.012   0.001   PHE R 139 
 TYR   0.009   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06085 (  160)
  hydrogen bonds       : angle       3.86870 (  480)
  SS BOND              : bond        0.00023 (    1)
  SS BOND              : angle       0.26791 (    2)
  covalent geometry    : bond        0.00298 ( 2159)
  covalent geometry    : angle       0.49419 ( 2961)

*********************** 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
  25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 19
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7511 (mtt) cc_final: 0.7210 (mtt)
  outliers start: 6
  outliers final: 4
  residues processed: 23
  average time/residue: 0.1659
  time to fit residues: 4.5825
Evaluate side-chains
  20 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 16
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  182 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:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0570
   chunk 22 optimal weight:    0.1980
   chunk 17 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.4298

-------------------------------------------------------------------------------
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 = 0.3638 r_free = 0.3638 target = 0.146940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.132655 restraints weight = 3076.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.136117 restraints weight = 1745.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.138621 restraints weight = 981.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.1306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   2160  Z= 0.121
  Angle     :  0.473   8.007   2963  Z= 0.259
  Chirality :  0.039   0.127    364
  Planarity :  0.003   0.026    358
  Dihedral  :  4.235  17.645    311
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 1.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 12.00 %
    Favored  : 86.00 %
  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:  2.48 (0.51), residues: 277
  helix:  2.81 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.33 (0.69), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R 178 
 PHE   0.008   0.001   PHE R 139 
 TYR   0.009   0.001   TYR R 185 
 ARG   0.001   0.000   ARG R 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05407 (  160)
  hydrogen bonds       : angle       3.74009 (  480)
  SS BOND              : bond        0.00037 (    1)
  SS BOND              : angle       0.22443 (    2)
  covalent geometry    : bond        0.00245 ( 2159)
  covalent geometry    : angle       0.47268 ( 2961)

*********************** 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
  22 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 18
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7435 (mtt) cc_final: 0.7132 (mtt)
  outliers start: 4
  outliers final: 3
  residues processed: 21
  average time/residue: 0.1403
  time to fit residues: 3.7010
Evaluate side-chains
  21 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 18
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  182 ILE
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 25 optimal weight:    0.4980
   chunk 16 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   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 = 0.3637 r_free = 0.3637 target = 0.146376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.131966 restraints weight = 3054.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.135358 restraints weight = 1769.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.137776 restraints weight = 1023.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.1364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2160  Z= 0.143
  Angle     :  0.513   9.101   2963  Z= 0.278
  Chirality :  0.039   0.124    364
  Planarity :  0.004   0.026    358
  Dihedral  :  4.309  17.488    311
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 13.00 %
    Favored  : 85.00 %
  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:  2.37 (0.51), residues: 277
  helix:  2.72 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.32 (0.70), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.011   0.001   PHE R 139 
 TYR   0.009   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05997 (  160)
  hydrogen bonds       : angle       3.79643 (  480)
  SS BOND              : bond        0.00076 (    1)
  SS BOND              : angle       0.31237 (    2)
  covalent geometry    : bond        0.00310 ( 2159)
  covalent geometry    : angle       0.51264 ( 2961)

*********************** 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
  24 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 20
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7498 (mtt) cc_final: 0.7193 (mtt)
  outliers start: 4
  outliers final: 4
  residues processed: 23
  average time/residue: 0.1651
  time to fit residues: 4.5647
Evaluate side-chains
  23 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  182 ILE
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 0 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0980
   chunk 27 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.144304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.129408 restraints weight = 3092.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.131955 restraints weight = 1728.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.133883 restraints weight = 1163.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.1399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2160  Z= 0.138
  Angle     :  0.506   9.303   2963  Z= 0.274
  Chirality :  0.039   0.124    364
  Planarity :  0.004   0.026    358
  Dihedral  :  4.294  17.469    311
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 13.00 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.51), residues: 277
  helix:  2.73 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.32 (0.70), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R 109 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R 139 
 TYR   0.009   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05917 (  160)
  hydrogen bonds       : angle       3.77240 (  480)
  SS BOND              : bond        0.00068 (    1)
  SS BOND              : angle       0.28066 (    2)
  covalent geometry    : bond        0.00296 ( 2159)
  covalent geometry    : angle       0.50593 ( 2961)

*********************** 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
  23 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 18
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7555 (mtt) cc_final: 0.7251 (mtt)
  outliers start: 5
  outliers final: 5
  residues processed: 21
  average time/residue: 0.0744
  time to fit residues: 2.2465
Evaluate side-chains
  23 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 18
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  182 ILE
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 26 optimal weight:    0.4980
   chunk 20 optimal weight:    0.7980
   chunk 12 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.143516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.128411 restraints weight = 3177.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.131052 restraints weight = 1754.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.132995 restraints weight = 1170.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.1447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2160  Z= 0.138
  Angle     :  0.518  10.420   2963  Z= 0.279
  Chirality :  0.039   0.123    364
  Planarity :  0.004   0.026    358
  Dihedral  :  4.279  17.450    311
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 13.50 %
    Favored  : 84.00 %
  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:  2.38 (0.51), residues: 277
  helix:  2.73 (0.34), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.30 (0.71), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R 139 
 TYR   0.009   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05925 (  160)
  hydrogen bonds       : angle       3.75885 (  480)
  SS BOND              : bond        0.00064 (    1)
  SS BOND              : angle       0.29662 (    2)
  covalent geometry    : bond        0.00298 ( 2159)
  covalent geometry    : angle       0.51792 ( 2961)

*********************** 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
  25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 20
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7568 (mtt) cc_final: 0.7262 (mtt)
  outliers start: 5
  outliers final: 5
  residues processed: 22
  average time/residue: 0.1180
  time to fit residues: 3.3233
Evaluate side-chains
  24 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 19
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  182 ILE
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 1 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 7 optimal weight:    0.4980
   chunk 0 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0170
   chunk 26 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.5818

-------------------------------------------------------------------------------
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 = 0.3611 r_free = 0.3611 target = 0.143631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.128705 restraints weight = 3135.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.131223 restraints weight = 1737.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.133108 restraints weight = 1178.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.1476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2160  Z= 0.137
  Angle     :  0.515  10.637   2963  Z= 0.277
  Chirality :  0.039   0.123    364
  Planarity :  0.004   0.026    358
  Dihedral  :  4.255  17.447    311
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.50 %
    Favored  : 83.00 %
  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:  2.44 (0.52), residues: 277
  helix:  2.75 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.22 (0.72), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R 139 
 TYR   0.009   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05887 (  160)
  hydrogen bonds       : angle       3.74376 (  480)
  SS BOND              : bond        0.00068 (    1)
  SS BOND              : angle       0.29129 (    2)
  covalent geometry    : bond        0.00294 ( 2159)
  covalent geometry    : angle       0.51533 ( 2961)

*********************** 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
  25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 20
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7576 (mtt) cc_final: 0.7268 (mtt)
  outliers start: 5
  outliers final: 5
  residues processed: 22
  average time/residue: 0.1323
  time to fit residues: 3.6687
Evaluate side-chains
  25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 20
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  182 ILE
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 3 optimal weight:    0.4980
   chunk 20 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 14 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 = 0.3618 r_free = 0.3618 target = 0.144325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.129563 restraints weight = 3116.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.132197 restraints weight = 1744.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.133873 restraints weight = 1164.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.1503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2160  Z= 0.141
  Angle     :  0.528  10.976   2963  Z= 0.283
  Chirality :  0.039   0.122    364
  Planarity :  0.004   0.027    358
  Dihedral  :  4.263  17.434    311
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.50 %
    Favored  : 83.00 %
  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:  2.43 (0.52), residues: 277
  helix:  2.74 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.20 (0.74), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R 139 
 TYR   0.008   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05991 (  160)
  hydrogen bonds       : angle       3.75928 (  480)
  SS BOND              : bond        0.00094 (    1)
  SS BOND              : angle       0.30336 (    2)
  covalent geometry    : bond        0.00305 ( 2159)
  covalent geometry    : angle       0.52779 ( 2961)

********************** 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
  24 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 19
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7580 (mtt) cc_final: 0.7278 (mtt)
  outliers start: 5
  outliers final: 5
  residues processed: 21
  average time/residue: 0.0830
  time to fit residues: 2.4719
Evaluate side-chains
  24 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 19
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  182 ILE
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0030
   overall best weight:    0.5190

-------------------------------------------------------------------------------
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 = 0.3611 r_free = 0.3611 target = 0.143672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.128627 restraints weight = 3131.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.131434 restraints weight = 1703.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.133236 restraints weight = 1117.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
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      :  0.003   0.036   2160  Z= 0.130
  Angle     :  0.510  10.860   2963  Z= 0.273
  Chirality :  0.039   0.122    364
  Planarity :  0.004   0.026    358
  Dihedral  :  4.206  17.422    311
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.50 %
    Favored  : 83.00 %
  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:  2.52 (0.52), residues: 277
  helix:  2.80 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.16 (0.74), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.008   0.001   PHE R 139 
 TYR   0.011   0.001   TYR R 185 
 ARG   0.001   0.000   ARG R 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05683 (  160)
  hydrogen bonds       : angle       3.70718 (  480)
  SS BOND              : bond        0.00035 (    1)
  SS BOND              : angle       0.28608 (    2)
  covalent geometry    : bond        0.00273 ( 2159)
  covalent geometry    : angle       0.51054 ( 2961)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1135.97 seconds
wall clock time: 20 minutes 44.99 seconds (1244.99 seconds total)