Starting phenix.real_space_refine
on Fri Aug 22 12:38:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggs_40019/08_2025/8ggs_40019.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggs_40019/08_2025/8ggs_40019.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggs_40019/08_2025/8ggs_40019.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggs_40019/08_2025/8ggs_40019.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ggs_40019/08_2025/8ggs_40019.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggs_40019/08_2025/8ggs_40019.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    1415      2.51       5
     N     331      2.21       5
     O     353      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2114
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2099
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2099
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 163
          Unresolved non-hydrogen angles: 200
          Unresolved non-hydrogen dihedrals: 135
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'TRP:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 7, 'ASP:plan': 4, 'ARG:plan': 6, 'HIS:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 99
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.74, per 1000 atoms: 0.35
  Number of scatterers: 2114
  At special positions: 0
  Unit cell: (56.4005, 82.4315, 62.4744, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      15     16.00
     O     353      8.00
     N     331      7.00
     C    1415      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.15
  Conformation dependent library (CDL) restraints added in 55.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 0 sheets defined
      87.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.04
  Creating SS restraints...
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 3.711A  pdb=" N   GLY R  37 " --> pdb=" O   VAL R  33 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 97
      removed outlier: 4.027A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 4.270A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER R 165 " --> pdb=" O   SER R 161 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 237
      removed outlier: 3.729A  pdb=" N   SER R 236 " --> pdb=" O   LYS R 232 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 287
      removed outlier: 3.877A  pdb=" N   THR R 274 " --> pdb=" O   LYS R 270 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ILE R 278 " --> pdb=" O   THR R 274 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 288 through 299
      removed outlier: 3.618A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 318
      removed outlier: 3.613A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 321 through 327
    Processing helix  chain 'R' and resid 329 through 340

    167 hydrogen bonds defined for protein.
    501 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.22

  Time building geometry restraints manager: 0.19 seconds

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

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

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

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.60: 1086
       12.60 -    25.19: 97
       25.19 -    37.79: 43
       37.79 -    50.38: 6
       50.38 -    62.98: 3
  Dihedral angle restraints: 1235
    sinusoidal: 407
      harmonic: 828
  Sorted by residual:
  dihedral pdb=" CA  PHE R 208 "
           pdb=" C   PHE R 208 "
           pdb=" N   TYR R 209 "
           pdb=" CA  TYR R 209 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.65  -18.35     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CA  ALA R  85 "
           pdb=" C   ALA R  85 "
           pdb=" N   VAL R  86 "
           pdb=" CA  VAL R  86 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.54  -15.46     0      5.00e+00 4.00e-02 9.56e+00
  dihedral pdb=" CB  MET R  36 "
           pdb=" CG  MET R  36 "
           pdb=" SD  MET R  36 "
           pdb=" CE  MET R  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  117.62  -57.62     3      1.50e+01 4.44e-03 9.44e+00
  ... (remaining 1232 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 246
       0.033 -    0.066: 89
       0.066 -    0.099: 29
       0.099 -    0.132: 3
       0.132 -    0.165: 1
  Chirality restraints: 368
  Sorted by residual:
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.56   -0.16 2.00e-01 2.50e+01 6.78e-01
  chirality pdb=" CA  PRO R 288 "
            pdb=" N   PRO R 288 "
            pdb=" C   PRO R 288 "
            pdb=" CB  PRO R 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.10 2.00e-01 2.50e+01 2.74e-01
  chirality pdb=" CA  PRO R  88 "
            pdb=" N   PRO R  88 "
            pdb=" C   PRO R  88 "
            pdb=" CB  PRO R  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.62    0.10 2.00e-01 2.50e+01 2.62e-01
  ... (remaining 365 not shown)

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

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

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.030
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     3.090
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   2171  Z= 0.221
  Angle     :  0.563   5.833   2981  Z= 0.317
  Chirality :  0.038   0.165    368
  Planarity :  0.004   0.044    357
  Dihedral  : 12.384  62.978    694
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.32 (0.50), residues: 277
  helix:  2.47 (0.35), residues: 209
  sheet:  None (None), residues: 0
  loop : -1.62 (0.71), residues: 68

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 2170)
  covalent geometry    : angle       0.56228 ( 2979)
  SS BOND              : bond        0.00168 (    1)
  SS BOND              : angle       1.29381 (    2)
  hydrogen bonds       : bond        0.16457 (  167)
  hydrogen bonds       : angle       4.97814 (  501)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.050 
Fit side-chains
REVERT: R   63 ARG cc_start: 0.7022 (mtm180) cc_final: 0.5599 (mpt180)
REVERT: R   84 LEU cc_start: 0.8143 (mm) cc_final: 0.7740 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0597
  time to fit residues: 2.1631
Evaluate side-chains
  24 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.127649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.113411 restraints weight = 3104.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.115913 restraints weight = 1605.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.117725 restraints weight = 1023.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.118885 restraints weight = 742.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.119731 restraints weight = 594.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.1262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2171  Z= 0.151
  Angle     :  0.493   4.865   2981  Z= 0.276
  Chirality :  0.040   0.114    368
  Planarity :  0.004   0.029    357
  Dihedral  :  4.392  18.290    309
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 12.14 %
    Favored  : 86.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.39 (0.50), residues: 277
  helix:  2.44 (0.34), residues: 222
  sheet:  None (None), residues: 0
  loop : -2.24 (0.68), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R  63 
 TYR   0.009   0.001   TYR R 308 
 PHE   0.010   0.001   PHE R 282 
 TRP   0.005   0.001   TRP R 313 
 HIS   0.003   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 2170)
  covalent geometry    : angle       0.49259 ( 2979)
  SS BOND              : bond        0.00239 (    1)
  SS BOND              : angle       1.07297 (    2)
  hydrogen bonds       : bond        0.06745 (  167)
  hydrogen bonds       : angle       3.86963 (  501)

*********************** 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
  31 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.075 
Fit side-chains
   revert: symmetry clash
REVERT: R   63 ARG cc_start: 0.7317 (mtm180) cc_final: 0.5615 (mpt180)
REVERT: R   84 LEU cc_start: 0.8161 (mm) cc_final: 0.7609 (mm)
REVERT: R  205 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7528 (mp)
  outliers start: 3
  outliers final: 2
  residues processed: 30
  average time/residue: 0.0927
  time to fit residues: 3.1593
Evaluate side-chains
  28 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  233 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 21 optimal weight:    0.0040
   chunk 6 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.5992

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

Flipped N/Q/H residues before XYZ refinement:
R 296 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.126785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.112747 restraints weight = 3127.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.115207 restraints weight = 1644.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.116973 restraints weight = 1052.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.118170 restraints weight = 765.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.118937 restraints weight = 610.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.1529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2171  Z= 0.141
  Angle     :  0.479   5.180   2981  Z= 0.264
  Chirality :  0.039   0.112    368
  Planarity :  0.003   0.028    357
  Dihedral  :  4.431  18.099    309
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 1.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 15.05 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.63 (0.50), residues: 277
  helix:  2.71 (0.34), residues: 220
  sheet:  None (None), residues: 0
  loop : -2.47 (0.63), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R  63 
 TYR   0.007   0.001   TYR R 308 
 PHE   0.009   0.001   PHE R 282 
 TRP   0.005   0.001   TRP R 313 
 HIS   0.003   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 2170)
  covalent geometry    : angle       0.47818 ( 2979)
  SS BOND              : bond        0.00207 (    1)
  SS BOND              : angle       1.08761 (    2)
  hydrogen bonds       : bond        0.06452 (  167)
  hydrogen bonds       : angle       3.75419 (  501)

*********************** 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
  34 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 27
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
REVERT: R   63 ARG cc_start: 0.7440 (mtm180) cc_final: 0.5640 (mpt180)
REVERT: R   84 LEU cc_start: 0.8047 (mm) cc_final: 0.7452 (mm)
REVERT: R  151 ARG cc_start: 0.7425 (mtm-85) cc_final: 0.6321 (mmt-90)
REVERT: R  205 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7395 (mp)
  outliers start: 7
  outliers final: 6
  residues processed: 32
  average time/residue: 0.0912
  time to fit residues: 3.3125
Evaluate side-chains
  30 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 23
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 7 optimal weight:    0.1980
   chunk 18 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0070
   chunk 2 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0770
   overall best weight:    0.3156

-------------------------------------------------------------------------------
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 = 0.3437 r_free = 0.3437 target = 0.129128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.115039 restraints weight = 3054.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.117611 restraints weight = 1593.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.119294 restraints weight = 1010.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.120538 restraints weight = 740.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.121427 restraints weight = 589.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.1530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2171  Z= 0.117
  Angle     :  0.448   5.232   2981  Z= 0.246
  Chirality :  0.037   0.108    368
  Planarity :  0.003   0.026    357
  Dihedral  :  4.300  17.891    309
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 1.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 15.53 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.71 (0.51), residues: 277
  helix:  2.73 (0.34), residues: 222
  sheet:  None (None), residues: 0
  loop : -2.45 (0.65), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 151 
 TYR   0.005   0.001   TYR R 308 
 PHE   0.007   0.001   PHE R 282 
 TRP   0.005   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 2170)
  covalent geometry    : angle       0.44736 ( 2979)
  SS BOND              : bond        0.00176 (    1)
  SS BOND              : angle       0.97082 (    2)
  hydrogen bonds       : bond        0.05689 (  167)
  hydrogen bonds       : angle       3.63037 (  501)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 26
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
REVERT: R   63 ARG cc_start: 0.7415 (mtm180) cc_final: 0.5602 (mpt180)
REVERT: R   84 LEU cc_start: 0.8186 (mm) cc_final: 0.7585 (mm)
REVERT: R  151 ARG cc_start: 0.7355 (mtm-85) cc_final: 0.6400 (mmt-90)
REVERT: R  205 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7589 (mp)
  outliers start: 7
  outliers final: 5
  residues processed: 31
  average time/residue: 0.0922
  time to fit residues: 3.2753
Evaluate side-chains
  30 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 24
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  233 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 23 optimal weight:    0.2980
   chunk 25 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3397 r_free = 0.3397 target = 0.125563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.111451 restraints weight = 3110.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.113954 restraints weight = 1633.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.115689 restraints weight = 1042.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.116813 restraints weight = 761.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.117644 restraints weight = 613.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2171  Z= 0.143
  Angle     :  0.468   5.338   2981  Z= 0.259
  Chirality :  0.038   0.115    368
  Planarity :  0.003   0.027    357
  Dihedral  :  4.353  17.897    309
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 1.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 17.48 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.73 (0.50), residues: 277
  helix:  2.80 (0.34), residues: 220
  sheet:  None (None), residues: 0
  loop : -2.56 (0.62), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG R  63 
 TYR   0.007   0.001   TYR R 308 
 PHE   0.009   0.001   PHE R 282 
 TRP   0.004   0.001   TRP R 109 
 HIS   0.002   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 2170)
  covalent geometry    : angle       0.46761 ( 2979)
  SS BOND              : bond        0.00240 (    1)
  SS BOND              : angle       0.97997 (    2)
  hydrogen bonds       : bond        0.06330 (  167)
  hydrogen bonds       : angle       3.68473 (  501)

*********************** 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
  33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 26
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
REVERT: R   63 ARG cc_start: 0.7470 (mtm180) cc_final: 0.5765 (mmt180)
REVERT: R   84 LEU cc_start: 0.8171 (mm) cc_final: 0.7565 (mm)
REVERT: R  151 ARG cc_start: 0.7393 (mtm-85) cc_final: 0.6421 (mmt-90)
REVERT: R  205 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7544 (mp)
  outliers start: 7
  outliers final: 6
  residues processed: 31
  average time/residue: 0.0951
  time to fit residues: 3.3580
Evaluate side-chains
  31 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 24
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  233 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 17 optimal weight:    0.3980
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0980
   chunk 12 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3400 r_free = 0.3400 target = 0.125679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.111568 restraints weight = 3084.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.113985 restraints weight = 1634.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.115702 restraints weight = 1051.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.116933 restraints weight = 776.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.117763 restraints weight = 615.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2171  Z= 0.135
  Angle     :  0.463   5.322   2981  Z= 0.257
  Chirality :  0.038   0.112    368
  Planarity :  0.003   0.028    357
  Dihedral  :  4.329  17.774    309
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 19.90 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.77 (0.50), residues: 277
  helix:  2.83 (0.34), residues: 220
  sheet:  None (None), residues: 0
  loop : -2.52 (0.61), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 151 
 TYR   0.007   0.001   TYR R 308 
 PHE   0.008   0.001   PHE R 282 
 TRP   0.004   0.001   TRP R 109 
 HIS   0.002   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 2170)
  covalent geometry    : angle       0.46274 ( 2979)
  SS BOND              : bond        0.00238 (    1)
  SS BOND              : angle       1.00601 (    2)
  hydrogen bonds       : bond        0.06226 (  167)
  hydrogen bonds       : angle       3.66095 (  501)

*********************** 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
  33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 25
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
REVERT: R   63 ARG cc_start: 0.7606 (mtm180) cc_final: 0.5723 (mmt180)
REVERT: R   84 LEU cc_start: 0.8016 (mm) cc_final: 0.7398 (mm)
REVERT: R  151 ARG cc_start: 0.7327 (mtm-85) cc_final: 0.6263 (mmt-90)
REVERT: R  205 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7409 (mp)
  outliers start: 8
  outliers final: 6
  residues processed: 31
  average time/residue: 0.0935
  time to fit residues: 3.2554
Evaluate side-chains
  32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 25
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  233 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
R 296 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.123553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.108944 restraints weight = 3136.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.111526 restraints weight = 1638.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.113323 restraints weight = 1039.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.114499 restraints weight = 754.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.115372 restraints weight = 603.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.1935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2171  Z= 0.162
  Angle     :  0.493   5.352   2981  Z= 0.275
  Chirality :  0.039   0.116    368
  Planarity :  0.003   0.029    357
  Dihedral  :  4.440  17.832    309
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 18.93 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.71 (0.50), residues: 277
  helix:  2.79 (0.34), residues: 220
  sheet:  None (None), residues: 0
  loop : -2.54 (0.62), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG R  63 
 TYR   0.008   0.001   TYR R 308 
 PHE   0.010   0.001   PHE R 282 
 TRP   0.004   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 2170)
  covalent geometry    : angle       0.49241 ( 2979)
  SS BOND              : bond        0.00285 (    1)
  SS BOND              : angle       1.00667 (    2)
  hydrogen bonds       : bond        0.06827 (  167)
  hydrogen bonds       : angle       3.75730 (  501)

*********************** 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
  36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 25
  time to evaluate  : 0.077 
Fit side-chains
   revert: symmetry clash
REVERT: R   63 ARG cc_start: 0.7681 (mtm180) cc_final: 0.5779 (mmt180)
REVERT: R   84 LEU cc_start: 0.8041 (mm) cc_final: 0.7402 (mm)
REVERT: R  205 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7372 (mp)
  outliers start: 11
  outliers final: 8
  residues processed: 32
  average time/residue: 0.0911
  time to fit residues: 3.3081
Evaluate side-chains
  33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 24
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain R residue  126 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0980
   chunk 14 optimal weight:    0.0870
   chunk 10 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.4358

-------------------------------------------------------------------------------
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 = 0.3398 r_free = 0.3398 target = 0.125667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.111687 restraints weight = 3106.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.114135 restraints weight = 1658.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.115866 restraints weight = 1064.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.117014 restraints weight = 780.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.117855 restraints weight = 624.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2171  Z= 0.127
  Angle     :  0.464   5.306   2981  Z= 0.257
  Chirality :  0.038   0.108    368
  Planarity :  0.003   0.028    357
  Dihedral  :  4.335  17.812    309
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 1.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 19.90 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.83 (0.50), residues: 277
  helix:  2.87 (0.34), residues: 220
  sheet:  None (None), residues: 0
  loop : -2.47 (0.62), residues: 57

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 2170)
  covalent geometry    : angle       0.46335 ( 2979)
  SS BOND              : bond        0.00214 (    1)
  SS BOND              : angle       0.98618 (    2)
  hydrogen bonds       : bond        0.06186 (  167)
  hydrogen bonds       : angle       3.63267 (  501)

*********************** 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
  36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 27
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
REVERT: R   63 ARG cc_start: 0.7672 (mtm180) cc_final: 0.5811 (mmt180)
REVERT: R   84 LEU cc_start: 0.8187 (mm) cc_final: 0.7569 (mm)
REVERT: R  151 ARG cc_start: 0.7396 (mtm-85) cc_final: 0.6419 (mmt-90)
REVERT: R  205 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7637 (mp)
  outliers start: 9
  outliers final: 7
  residues processed: 30
  average time/residue: 0.1085
  time to fit residues: 3.6562
Evaluate side-chains
  35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 27
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain R residue  126 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  233 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 24 optimal weight:    0.1980
   chunk 1 optimal weight:    0.8980
   chunk 21 optimal weight:    0.4980
   chunk 12 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 18 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.125147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.111107 restraints weight = 3102.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.113549 restraints weight = 1659.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.115290 restraints weight = 1077.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.116497 restraints weight = 786.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.117133 restraints weight = 625.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2171  Z= 0.132
  Angle     :  0.462   5.323   2981  Z= 0.255
  Chirality :  0.038   0.111    368
  Planarity :  0.003   0.028    357
  Dihedral  :  4.283  17.849    309
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 19.42 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.84 (0.50), residues: 277
  helix:  2.85 (0.34), residues: 221
  sheet:  None (None), residues: 0
  loop : -2.45 (0.62), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R  63 
 TYR   0.007   0.001   TYR R 308 
 PHE   0.008   0.001   PHE R 282 
 TRP   0.004   0.001   TRP R 109 
 HIS   0.002   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 2170)
  covalent geometry    : angle       0.46109 ( 2979)
  SS BOND              : bond        0.00261 (    1)
  SS BOND              : angle       1.03023 (    2)
  hydrogen bonds       : bond        0.06077 (  167)
  hydrogen bonds       : angle       3.63478 (  501)

*********************** 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
  36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 27
  time to evaluate  : 0.079 
Fit side-chains
   revert: symmetry clash
REVERT: R   63 ARG cc_start: 0.7671 (mtm180) cc_final: 0.5736 (mmt180)
REVERT: R   84 LEU cc_start: 0.7958 (mm) cc_final: 0.7322 (mm)
REVERT: R  151 ARG cc_start: 0.7341 (mtm-85) cc_final: 0.6207 (mmt-90)
REVERT: R  205 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7373 (mp)
  outliers start: 9
  outliers final: 6
  residues processed: 30
  average time/residue: 0.0907
  time to fit residues: 3.1086
Evaluate side-chains
  34 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 27
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain R residue  126 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0470
   chunk 6 optimal weight:    0.6980
   chunk 14 optimal weight:    0.1980
   chunk 1 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.4278

-------------------------------------------------------------------------------
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 = 0.3418 r_free = 0.3418 target = 0.126962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.112923 restraints weight = 3123.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.115398 restraints weight = 1658.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.117181 restraints weight = 1068.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.118412 restraints weight = 774.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.119168 restraints weight = 612.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   2171  Z= 0.120
  Angle     :  0.449   5.324   2981  Z= 0.246
  Chirality :  0.037   0.108    368
  Planarity :  0.003   0.028    357
  Dihedral  :  4.185  17.714    309
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 19.90 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.98 (0.50), residues: 277
  helix:  2.95 (0.34), residues: 221
  sheet:  None (None), residues: 0
  loop : -2.45 (0.62), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R  63 
 TYR   0.008   0.001   TYR R 185 
 PHE   0.007   0.001   PHE R 282 
 TRP   0.004   0.001   TRP R 109 
 HIS   0.002   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 2170)
  covalent geometry    : angle       0.44856 ( 2979)
  SS BOND              : bond        0.00237 (    1)
  SS BOND              : angle       1.09239 (    2)
  hydrogen bonds       : bond        0.05626 (  167)
  hydrogen bonds       : angle       3.58033 (  501)

********************** 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
  33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 25
  time to evaluate  : 0.077 
Fit side-chains
   revert: symmetry clash
REVERT: R   63 ARG cc_start: 0.7633 (mtm180) cc_final: 0.5702 (mmt180)
REVERT: R   84 LEU cc_start: 0.7938 (mm) cc_final: 0.7301 (mm)
REVERT: R  151 ARG cc_start: 0.7322 (mtm-85) cc_final: 0.6144 (mmt-90)
REVERT: R  205 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7370 (mp)
  outliers start: 8
  outliers final: 6
  residues processed: 29
  average time/residue: 0.0907
  time to fit residues: 2.9605
Evaluate side-chains
  32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 25
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   34 VAL
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain R residue  126 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 18 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 17 optimal weight:    0.1980
   chunk 21 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 0 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.125318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.111298 restraints weight = 3138.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.113756 restraints weight = 1680.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.115483 restraints weight = 1089.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.116695 restraints weight = 794.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.117420 restraints weight = 632.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2171  Z= 0.133
  Angle     :  0.461   5.324   2981  Z= 0.254
  Chirality :  0.038   0.111    368
  Planarity :  0.003   0.028    357
  Dihedral  :  4.224  17.715    309
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 20.39 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.93 (0.50), residues: 277
  helix:  2.93 (0.34), residues: 221
  sheet:  None (None), residues: 0
  loop : -2.49 (0.62), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R  63 
 TYR   0.007   0.001   TYR R 308 
 PHE   0.008   0.001   PHE R 282 
 TRP   0.004   0.001   TRP R 109 
 HIS   0.002   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 2170)
  covalent geometry    : angle       0.46076 ( 2979)
  SS BOND              : bond        0.00267 (    1)
  SS BOND              : angle       1.02021 (    2)
  hydrogen bonds       : bond        0.06048 (  167)
  hydrogen bonds       : angle       3.62028 (  501)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 647.91 seconds
wall clock time: 13 minutes 17.52 seconds (797.52 seconds total)