Starting phenix.real_space_refine
on Fri May  9 13:18:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggp_40016/05_2025/8ggp_40016.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggp_40016/05_2025/8ggp_40016.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ggp_40016/05_2025/8ggp_40016.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggp_40016/05_2025/8ggp_40016.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggp_40016/05_2025/8ggp_40016.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggp_40016/05_2025/8ggp_40016.cif"
  }
  resolution = 3.2
  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=   0.027
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    1394      2.51       5
     N     328      2.21       5
     O     340      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 2075
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2060
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2060
          Classifications: {'peptide': 280}
          Incomplete info: {'truncation_to_alanine': 54}
          Link IDs: {'PTRANS': 7, 'TRANS': 272}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 196
          Unresolved non-hydrogen angles: 239
          Unresolved non-hydrogen dihedrals: 162
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 115
    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: 2.26, per 1000 atoms: 1.09
  Number of scatterers: 2075
  At special positions: 0
  Unit cell: (57.2682, 80.6961, 62.4744, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      13     16.00
     O     340      8.00
     N     328      7.00
     C    1394      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: 0.51
  Conformation dependent library (CDL) restraints added in 243.7 milliseconds
  

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 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:
      15 helices and 0 sheets defined
      90.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 3.578A  pdb=" N   GLY R  37 " --> pdb=" O   VAL R  33 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 62 through 65
      removed outlier: 3.781A  pdb=" N   GLN R  65 " --> pdb=" O   GLU R  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 62 through 65'
    Processing helix  chain 'R' and resid 66 through 85
      removed outlier: 4.135A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 85 through 97
      removed outlier: 4.202A  pdb=" N   PHE R  89 " --> pdb=" O   ALA R  85 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 3.501A  pdb=" N   SER R 120 " --> pdb=" O   CYS R 116 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   CYS R 125 " --> pdb=" O   ILE R 121 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.778A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
      removed outlier: 4.091A  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: 3.520A  pdb=" N   ILE R 182 " --> pdb=" O   HIS R 178 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 196 through 208
      removed outlier: 3.718A  pdb=" N   VAL R 206 " --> pdb=" O   ALA R 202 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 237
    Processing helix  chain 'R' and resid 271 through 299
      removed outlier: 4.093A  pdb=" N   THR R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.508A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ILE R 298 " --> pdb=" O   ILE R 294 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.821A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 318 through 320
      No H-bonds generated for 'chain 'R' and resid 318 through 320'
    Processing helix  chain 'R' and resid 321 through 327
    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: 0.60 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 615
        1.34 -     1.46: 495
        1.46 -     1.58: 1004
        1.58 -     1.70: 0
        1.70 -     1.82: 17
  Bond restraints: 2131
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.448 -0.051 2.00e-02 2.50e+03 6.50e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.442 -0.048 2.00e-02 2.50e+03 5.73e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.569 -0.046 2.00e-02 2.50e+03 5.25e+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=" CAE G1I R 501 "
       pdb=" CAG G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.506  1.537 -0.031 2.00e-02 2.50e+03 2.44e+00
  ... (remaining 2126 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.08: 2813
        1.08 -     2.16: 100
        2.16 -     3.25: 8
        3.25 -     4.33: 7
        4.33 -     5.41: 5
  Bond angle restraints: 2933
  Sorted by residual:
  angle pdb=" C   SER R 207 "
        pdb=" N   PHE R 208 "
        pdb=" CA  PHE R 208 "
      ideal   model   delta    sigma   weight residual
     122.46  119.21    3.25 1.80e+00 3.09e-01 3.26e+00
  angle pdb=" CAE G1I R 501 "
        pdb=" CAG G1I R 501 "
        pdb=" CAH G1I R 501 "
      ideal   model   delta    sigma   weight residual
     112.63  118.04   -5.41 3.00e+00 1.11e-01 3.25e+00
  angle pdb=" N   VAL R  87 "
        pdb=" CA  VAL R  87 "
        pdb=" C   VAL R  87 "
      ideal   model   delta    sigma   weight residual
     108.88  112.53   -3.65 2.16e+00 2.14e-01 2.86e+00
  angle pdb=" C   THR R  96 "
        pdb=" N   LYS R  97 "
        pdb=" CA  LYS R  97 "
      ideal   model   delta    sigma   weight residual
     124.31  127.13   -2.82 1.67e+00 3.59e-01 2.85e+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  115.86   -4.97 3.00e+00 1.11e-01 2.75e+00
  ... (remaining 2928 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.65: 1053
       12.65 -    25.30: 111
       25.30 -    37.95: 28
       37.95 -    50.60: 12
       50.60 -    63.25: 1
  Dihedral angle restraints: 1205
    sinusoidal: 378
      harmonic: 827
  Sorted by residual:
  dihedral pdb=" CA  PHE R 208 "
           pdb=" C   PHE R 208 "
           pdb=" N   TYR R 209 "
           pdb=" CA  TYR R 209 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.43  -17.57     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  VAL R 295 "
           pdb=" C   VAL R 295 "
           pdb=" N   HIS R 296 "
           pdb=" CA  HIS R 296 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.96  -15.04     0      5.00e+00 4.00e-02 9.04e+00
  dihedral pdb=" CA  ARG R 151 "
           pdb=" CB  ARG R 151 "
           pdb=" CG  ARG R 151 "
           pdb=" CD  ARG R 151 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -130.02  -49.98     3      1.50e+01 4.44e-03 8.84e+00
  ... (remaining 1202 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 226
       0.030 -    0.059: 101
       0.059 -    0.089: 25
       0.089 -    0.119: 14
       0.119 -    0.149: 1
  Chirality restraints: 367
  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 5.51e-01
  chirality pdb=" CA  TRP R 313 "
            pdb=" N   TRP R 313 "
            pdb=" C   TRP R 313 "
            pdb=" CB  TRP R 313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.42e-01
  chirality pdb=" CA  PRO R 138 "
            pdb=" N   PRO R 138 "
            pdb=" C   PRO R 138 "
            pdb=" CB  PRO R 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 3.05e-01
  ... (remaining 364 not shown)

  Planarity restraints: 351
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 313 "   -0.007 2.00e-02 2.50e+03   9.51e-03 2.26e+00
        pdb=" CG  TRP R 313 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 313 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 313 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 313 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 313 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 313 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 313 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 313 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 313 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 322 "    0.016 5.00e-02 4.00e+02   2.37e-02 8.98e-01
        pdb=" N   PRO R 323 "   -0.041 5.00e-02 4.00e+02
        pdb=" CA  PRO R 323 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO R 323 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 210 "    0.014 5.00e-02 4.00e+02   2.10e-02 7.03e-01
        pdb=" N   PRO R 211 "   -0.036 5.00e-02 4.00e+02
        pdb=" CA  PRO R 211 "    0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO R 211 "    0.012 5.00e-02 4.00e+02
  ... (remaining 348 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 590
        2.82 -     3.34: 2039
        3.34 -     3.86: 3309
        3.86 -     4.38: 3397
        4.38 -     4.90: 6312
  Nonbonded interactions: 15647
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAL G1I R 501 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   LEU R  64 "
            pdb=" ND2 ASN R  69 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" O   SER R 137 "
            pdb=" OG  SER R 137 "
     model   vdw
     2.344 3.040
  nonbonded pdb=" O   THR R 189 "
            pdb=" OG1 THR R 189 "
     model   vdw
     2.491 3.040
  nonbonded pdb=" OD1 ASN R 196 "
            pdb=" N   GLN R 197 "
     model   vdw
     2.513 3.120
  ... (remaining 15642 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.440
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     10.320
  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:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
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   0.051   2132  Z= 0.189
  Angle     :  0.522   5.412   2935  Z= 0.285
  Chirality :  0.039   0.149    367
  Planarity :  0.003   0.024    351
  Dihedral  : 12.492  63.247    664
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  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:  1.89 (0.51), residues: 276
  helix:  1.93 (0.35), residues: 220
  sheet:  None (None), residues: 0
  loop : -1.52 (0.69), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP R 313 
 HIS   0.003   0.001   HIS R  93 
 PHE   0.010   0.001   PHE R 217 
 TYR   0.010   0.001   TYR R 174 
 ARG   0.001   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16196 (  166)
  hydrogen bonds       : angle       5.18511 (  498)
  SS BOND              : bond        0.00127 (    1)
  SS BOND              : angle       1.45246 (    2)
  covalent geometry    : bond        0.00386 ( 2131)
  covalent geometry    : angle       0.52046 ( 2933)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 19
  average time/residue: 0.1348
  time to fit residues: 3.3363
Evaluate side-chains
  17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    0.4980
   chunk 14 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   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 = 0.3478 r_free = 0.3478 target = 0.132673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.116627 restraints weight = 2932.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 1.71
r_work: 0.3261 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3159 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.0807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2132  Z= 0.146
  Angle     :  0.481   5.464   2935  Z= 0.271
  Chirality :  0.038   0.130    367
  Planarity :  0.003   0.022    351
  Dihedral  :  4.298  17.933    309
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 1.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  5.67 %
    Favored  : 93.81 %
  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:  2.27 (0.51), residues: 276
  helix:  2.15 (0.35), residues: 226
  sheet:  None (None), residues: 0
  loop : -1.66 (0.75), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 313 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R 217 
 TYR   0.007   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06276 (  166)
  hydrogen bonds       : angle       3.94270 (  498)
  SS BOND              : bond        0.00128 (    1)
  SS BOND              : angle       1.28593 (    2)
  covalent geometry    : bond        0.00312 ( 2131)
  covalent geometry    : angle       0.48024 ( 2933)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 17
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 18
  average time/residue: 0.1136
  time to fit residues: 2.7144
Evaluate side-chains
  16 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 15
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0270
   chunk 23 optimal weight:    0.0570
   chunk 16 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 7 optimal weight:    0.3980
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.3756

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.135972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.119723 restraints weight = 2851.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 1.81
r_work: 0.3319 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.1073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   2132  Z= 0.115
  Angle     :  0.437   5.369   2935  Z= 0.242
  Chirality :  0.037   0.124    367
  Planarity :  0.003   0.022    351
  Dihedral  :  4.129  17.913    309
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 1.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  :  8.25 %
    Favored  : 90.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.67 (0.51), residues: 276
  helix:  2.45 (0.35), residues: 226
  sheet:  None (None), residues: 0
  loop : -1.59 (0.77), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R  93 
 PHE   0.008   0.001   PHE R 217 
 TYR   0.006   0.001   TYR R 209 
 ARG   0.002   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05134 (  166)
  hydrogen bonds       : angle       3.62637 (  498)
  SS BOND              : bond        0.00135 (    1)
  SS BOND              : angle       1.20692 (    2)
  covalent geometry    : bond        0.00228 ( 2131)
  covalent geometry    : angle       0.43636 ( 2933)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 15
  time to evaluate  : 0.224 
Fit side-chains
REVERT: R   40 MET cc_start: 0.7175 (mtt) cc_final: 0.6924 (mtt)
  outliers start: 3
  outliers final: 2
  residues processed: 18
  average time/residue: 0.1110
  time to fit residues: 2.6948
Evaluate side-chains
  17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 15
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0570
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
R 178 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.133783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.117990 restraints weight = 2841.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 1.66
r_work: 0.3324 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.1137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2132  Z= 0.125
  Angle     :  0.444   5.439   2935  Z= 0.247
  Chirality :  0.037   0.124    367
  Planarity :  0.003   0.023    351
  Dihedral  :  4.131  17.658    309
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 1.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 12.37 %
    Favored  : 86.60 %
  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:  2.65 (0.51), residues: 276
  helix:  2.44 (0.35), residues: 226
  sheet:  None (None), residues: 0
  loop : -1.64 (0.78), residues: 50

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   0.008   0.001   PHE R 217 
 TYR   0.006   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05469 (  166)
  hydrogen bonds       : angle       3.59481 (  498)
  SS BOND              : bond        0.00172 (    1)
  SS BOND              : angle       1.06516 (    2)
  covalent geometry    : bond        0.00262 ( 2131)
  covalent geometry    : angle       0.44307 ( 2933)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.227 
Fit side-chains
REVERT: R   40 MET cc_start: 0.7140 (mtt) cc_final: 0.6900 (mtt)
  outliers start: 2
  outliers final: 2
  residues processed: 16
  average time/residue: 0.1105
  time to fit residues: 2.4184
Evaluate side-chains
  16 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 5 optimal weight:    0.4980
   chunk 12 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.130202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.113811 restraints weight = 2961.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.84
r_work: 0.3235 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.1189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   2132  Z= 0.163
  Angle     :  0.483   5.501   2935  Z= 0.272
  Chirality :  0.039   0.127    367
  Planarity :  0.003   0.026    351
  Dihedral  :  4.328  18.033    309
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 1.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 14.43 %
    Favored  : 84.54 %
  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 (0.51), residues: 276
  helix:  2.30 (0.35), residues: 226
  sheet:  None (None), residues: 0
  loop : -1.92 (0.74), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R 282 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06649 (  166)
  hydrogen bonds       : angle       3.77489 (  498)
  SS BOND              : bond        0.00210 (    1)
  SS BOND              : angle       1.19351 (    2)
  covalent geometry    : bond        0.00371 ( 2131)
  covalent geometry    : angle       0.48170 ( 2933)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.238 
Fit side-chains
REVERT: R   40 MET cc_start: 0.7343 (mtt) cc_final: 0.7079 (mtt)
  outliers start: 2
  outliers final: 2
  residues processed: 16
  average time/residue: 0.1154
  time to fit residues: 2.5317
Evaluate side-chains
  16 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 10 optimal weight:    0.3980
   chunk 6 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0980
   chunk 4 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 2 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.3575 r_free = 0.3575 target = 0.139883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.123866 restraints weight = 2797.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.81
r_work: 0.3268 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.1222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2132  Z= 0.124
  Angle     :  0.440   5.457   2935  Z= 0.245
  Chirality :  0.037   0.124    367
  Planarity :  0.003   0.026    351
  Dihedral  :  4.160  18.424    309
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 1.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 14.95 %
    Favored  : 84.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.66 (0.51), residues: 276
  helix:  2.48 (0.35), residues: 226
  sheet:  None (None), residues: 0
  loop : -1.83 (0.75), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.002   0.001   HIS R  93 
 PHE   0.008   0.001   PHE R 217 
 TYR   0.006   0.001   TYR R 209 
 ARG   0.002   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05556 (  166)
  hydrogen bonds       : angle       3.61028 (  498)
  SS BOND              : bond        0.00189 (    1)
  SS BOND              : angle       1.02373 (    2)
  covalent geometry    : bond        0.00253 ( 2131)
  covalent geometry    : angle       0.43913 ( 2933)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 15
  time to evaluate  : 0.229 
Fit side-chains
REVERT: R   40 MET cc_start: 0.7185 (mtt) cc_final: 0.6948 (mtt)
  outliers start: 2
  outliers final: 2
  residues processed: 17
  average time/residue: 0.1827
  time to fit residues: 3.8234
Evaluate side-chains
  17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 15
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 20 optimal weight:    0.2980
   chunk 27 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 11 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 = 0.3472 r_free = 0.3472 target = 0.132039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.115697 restraints weight = 2913.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 1.80
r_work: 0.3234 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
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      :  0.003   0.021   2132  Z= 0.141
  Angle     :  0.456   5.490   2935  Z= 0.255
  Chirality :  0.038   0.124    367
  Planarity :  0.003   0.027    351
  Dihedral  :  4.221  18.172    309
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 1.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 14.43 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.59 (0.51), residues: 276
  helix:  2.43 (0.34), residues: 226
  sheet:  None (None), residues: 0
  loop : -1.87 (0.75), residues: 50

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   0.009   0.001   PHE R 282 
 TYR   0.006   0.001   TYR R 199 
 ARG   0.002   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05986 (  166)
  hydrogen bonds       : angle       3.66174 (  498)
  SS BOND              : bond        0.00202 (    1)
  SS BOND              : angle       1.05310 (    2)
  covalent geometry    : bond        0.00309 ( 2131)
  covalent geometry    : angle       0.45576 ( 2933)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 15
  time to evaluate  : 0.215 
Fit side-chains
REVERT: R   40 MET cc_start: 0.7222 (mtt) cc_final: 0.6975 (mtt)
  outliers start: 4
  outliers final: 3
  residues processed: 19
  average time/residue: 0.1630
  time to fit residues: 3.7875
Evaluate side-chains
  18 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 15
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   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 = 0.3445 r_free = 0.3445 target = 0.129946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.113739 restraints weight = 2976.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 1.80
r_work: 0.3208 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.1283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2132  Z= 0.152
  Angle     :  0.464   5.508   2935  Z= 0.262
  Chirality :  0.038   0.125    367
  Planarity :  0.003   0.027    351
  Dihedral  :  4.293  18.219    309
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 1.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 14.95 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.50 (0.51), residues: 276
  helix:  2.42 (0.34), residues: 225
  sheet:  None (None), residues: 0
  loop : -2.07 (0.74), residues: 51

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   0.009   0.001   PHE R 282 
 TYR   0.006   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06335 (  166)
  hydrogen bonds       : angle       3.72333 (  498)
  SS BOND              : bond        0.00195 (    1)
  SS BOND              : angle       1.08626 (    2)
  covalent geometry    : bond        0.00341 ( 2131)
  covalent geometry    : angle       0.46328 ( 2933)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 14
  time to evaluate  : 0.239 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 17
  average time/residue: 0.1116
  time to fit residues: 2.5806
Evaluate side-chains
  17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 14
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.135574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.119336 restraints weight = 2945.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 1.86
r_work: 0.3226 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3118 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2132  Z= 0.151
  Angle     :  0.463   5.515   2935  Z= 0.261
  Chirality :  0.038   0.125    367
  Planarity :  0.003   0.027    351
  Dihedral  :  4.285  18.367    309
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 1.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 14.95 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.51), residues: 276
  helix:  2.38 (0.34), residues: 226
  sheet:  None (None), residues: 0
  loop : -2.04 (0.73), residues: 50

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   0.009   0.001   PHE R 282 
 TYR   0.006   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06290 (  166)
  hydrogen bonds       : angle       3.72029 (  498)
  SS BOND              : bond        0.00203 (    1)
  SS BOND              : angle       1.10905 (    2)
  covalent geometry    : bond        0.00335 ( 2131)
  covalent geometry    : angle       0.46270 ( 2933)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 14
  time to evaluate  : 0.219 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 17
  average time/residue: 0.1090
  time to fit residues: 2.5056
Evaluate side-chains
  17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 14
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 3 optimal weight:    0.3980
   chunk 20 optimal weight:    0.9980
   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 = 0.3534 r_free = 0.3534 target = 0.136277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.120244 restraints weight = 2856.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 1.83
r_work: 0.3228 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.1313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2132  Z= 0.143
  Angle     :  0.457   5.500   2935  Z= 0.256
  Chirality :  0.038   0.125    367
  Planarity :  0.003   0.027    351
  Dihedral  :  4.258  18.413    309
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 1.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 14.95 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.57 (0.51), residues: 276
  helix:  2.44 (0.34), residues: 226
  sheet:  None (None), residues: 0
  loop : -2.02 (0.73), residues: 50

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   0.009   0.001   PHE R 282 
 TYR   0.006   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06097 (  166)
  hydrogen bonds       : angle       3.69036 (  498)
  SS BOND              : bond        0.00212 (    1)
  SS BOND              : angle       1.08937 (    2)
  covalent geometry    : bond        0.00314 ( 2131)
  covalent geometry    : angle       0.45578 ( 2933)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 14
  time to evaluate  : 0.231 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 17
  average time/residue: 0.1027
  time to fit residues: 2.3743
Evaluate side-chains
  17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 14
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0670
   chunk 19 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.5118

-------------------------------------------------------------------------------
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 = 0.3522 r_free = 0.3522 target = 0.135697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.119424 restraints weight = 2910.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 1.87
r_work: 0.3273 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.1335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2132  Z= 0.128
  Angle     :  0.440   5.481   2935  Z= 0.246
  Chirality :  0.038   0.122    367
  Planarity :  0.003   0.027    351
  Dihedral  :  4.171  18.458    309
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 1.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 15.98 %
    Favored  : 82.47 %
  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:  2.71 (0.51), residues: 276
  helix:  2.53 (0.34), residues: 226
  sheet:  None (None), residues: 0
  loop : -1.92 (0.75), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R  93 
 PHE   0.008   0.001   PHE R 217 
 TYR   0.006   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05598 (  166)
  hydrogen bonds       : angle       3.59617 (  498)
  SS BOND              : bond        0.00187 (    1)
  SS BOND              : angle       1.02101 (    2)
  covalent geometry    : bond        0.00269 ( 2131)
  covalent geometry    : angle       0.43905 ( 2933)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1562.45 seconds
wall clock time: 27 minutes 58.62 seconds (1678.62 seconds total)