Starting phenix.real_space_refine
on Fri Aug 22 12:40:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggj_40010/08_2025/8ggj_40010.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggj_40010/08_2025/8ggj_40010.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ggj_40010/08_2025/8ggj_40010.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggj_40010/08_2025/8ggj_40010.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggj_40010/08_2025/8ggj_40010.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggj_40010/08_2025/8ggj_40010.cif"
  }
  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=   0.027
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      15      5.16       5
     C    1471      2.51       5
     N     351      2.21       5
     O     364      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: 2201
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2185
          Classifications: {'peptide': 286}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 7, 'TRANS': 278}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 120
          Unresolved non-hydrogen angles: 149
          Unresolved non-hydrogen dihedrals: 100
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 6, 'ASP:plan': 5, 'ASN:plan1': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 79
    Chain: "R"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 16
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 0.94, per 1000 atoms: 0.43
  Number of scatterers: 2201
  At special positions: 0
  Unit cell: (59.8713, 85.9023, 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     364      8.00
     N     351      7.00
     C    1471      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: 0.20
  Conformation dependent library (CDL) restraints added in 83.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  548

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 0 sheets defined
      86.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'R' and resid 31 through 61
      removed outlier: 3.581A  pdb=" N   GLY R  37 " --> pdb=" O   VAL R  33 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU R  53 " --> pdb=" O   PHE R  49 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   VAL R  54 " --> pdb=" O   GLY R  50 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ILE R  55 " --> pdb=" O   ASN R  51 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 86
      removed outlier: 4.463A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 86 through 97
    Processing helix  chain 'R' and resid 103 through 137
      removed outlier: 4.287A  pdb=" N   GLU R 107 " --> pdb=" O   ASN R 103 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   PHE R 108 " --> pdb=" O   PHE R 104 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ILE R 121 " --> pdb=" O   VAL R 117 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   GLU R 122 " --> pdb=" O   THR R 118 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   THR R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   LEU R 124 " --> pdb=" O   SER R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 163
      removed outlier: 3.775A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 166 through 171
    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
    Processing helix  chain 'R' and resid 269 through 281
      removed outlier: 3.821A  pdb=" N   THR R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 282 through 296
      Proline residue:  R 288  - end of helix
      removed outlier: 3.626A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 315
      removed outlier: 3.602A  pdb=" N   GLY R 315 " --> pdb=" O   LEU R 311 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 316 through 320
    Processing helix  chain 'R' and resid 321 through 327
    Processing helix  chain 'R' and resid 329 through 340

    160 hydrogen bonds defined for protein.
    474 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: 0.32

  Time building geometry restraints manager: 0.27 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 651
        1.34 -     1.46: 518
        1.46 -     1.58: 1068
        1.58 -     1.69: 0
        1.69 -     1.81: 21
  Bond restraints: 2258
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.449 -0.052 2.00e-02 2.50e+03 6.67e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.438 -0.044 2.00e-02 2.50e+03 4.89e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.566 -0.043 2.00e-02 2.50e+03 4.63e+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 4.33e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" OAK G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.353  1.319  0.034 2.00e-02 2.50e+03 2.85e+00
  ... (remaining 2253 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.11: 2971
        1.11 -     2.21: 95
        2.21 -     3.32: 12
        3.32 -     4.43: 7
        4.43 -     5.54: 6
  Bond angle restraints: 3091
  Sorted by residual:
  angle pdb=" C   THR R  96 "
        pdb=" N   LYS R  97 "
        pdb=" CA  LYS R  97 "
      ideal   model   delta    sigma   weight residual
     121.54  127.08   -5.54 1.91e+00 2.74e-01 8.40e+00
  angle pdb=" C   LEU R  84 "
        pdb=" N   ALA R  85 "
        pdb=" CA  ALA R  85 "
      ideal   model   delta    sigma   weight residual
     122.79  119.15    3.64 1.78e+00 3.16e-01 4.19e+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  117.92   -5.29 3.00e+00 1.11e-01 3.11e+00
  angle pdb=" N   SER R 236 "
        pdb=" CA  SER R 236 "
        pdb=" C   SER R 236 "
      ideal   model   delta    sigma   weight residual
     111.40  113.41   -2.01 1.22e+00 6.72e-01 2.72e+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  115.70   -4.81 3.00e+00 1.11e-01 2.58e+00
  ... (remaining 3086 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.64: 1067
       10.64 -    21.28: 140
       21.28 -    31.92: 59
       31.92 -    42.56: 23
       42.56 -    53.19: 5
  Dihedral angle restraints: 1294
    sinusoidal: 451
      harmonic: 843
  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 -160.78  -19.22     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CG  ARG R 175 "
           pdb=" CD  ARG R 175 "
           pdb=" NE  ARG R 175 "
           pdb=" CZ  ARG R 175 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  138.69   41.31     2      1.50e+01 4.44e-03 9.30e+00
  dihedral pdb=" CA  HIS R 178 "
           pdb=" C   HIS R 178 "
           pdb=" N   GLN R 179 "
           pdb=" CA  GLN R 179 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.98  -15.02     0      5.00e+00 4.00e-02 9.03e+00
  ... (remaining 1291 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 229
       0.030 -    0.060: 100
       0.060 -    0.089: 36
       0.089 -    0.119: 13
       0.119 -    0.149: 1
  Chirality restraints: 379
  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 5.56e-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    2.62    0.10 2.00e-01 2.50e+01 2.57e-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    2.62    0.10 2.00e-01 2.50e+01 2.52e-01
  ... (remaining 376 not shown)

  Planarity restraints: 368
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R  87 "   -0.022 5.00e-02 4.00e+02   3.35e-02 1.79e+00
        pdb=" N   PRO R  88 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO R  88 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO R  88 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 322 "    0.020 5.00e-02 4.00e+02   2.97e-02 1.41e+00
        pdb=" N   PRO R 323 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO R 323 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO R 323 "    0.017 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   2.37e-02 9.01e-01
        pdb=" N   PRO R 211 "   -0.041 5.00e-02 4.00e+02
        pdb=" CA  PRO R 211 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO R 211 "    0.013 5.00e-02 4.00e+02
  ... (remaining 365 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 464
        2.78 -     3.31: 2093
        3.31 -     3.84: 3475
        3.84 -     4.37: 3624
        4.37 -     4.90: 6840
  Nonbonded interactions: 16496
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAL G1I R 501 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" N   GLU R 306 "
            pdb=" OE1 GLU R 306 "
     model   vdw
     2.294 3.120
  nonbonded pdb=" O   SER R 111 "
            pdb=" OG  SER R 165 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" O   ILE R  47 "
            pdb=" ND2 ASN R  51 "
     model   vdw
     2.315 3.120
  nonbonded pdb=" OD2 ASP R 113 "
            pdb=" OAM G1I R 501 "
     model   vdw
     2.368 3.040
  ... (remaining 16491 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:             3.060
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     5.060
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
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   0.052   2259  Z= 0.184
  Angle     :  0.533   5.536   3093  Z= 0.287
  Chirality :  0.040   0.149    379
  Planarity :  0.004   0.033    368
  Dihedral  : 13.044  53.194    743
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 2.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.95 (0.52), residues: 282
  helix:  1.82 (0.36), residues: 220
  sheet:  None (None), residues: 0
  loop : -0.58 (0.83), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 239 
 TYR   0.010   0.001   TYR R 132 
 PHE   0.008   0.001   PHE R 240 
 TRP   0.011   0.001   TRP R 313 
 HIS   0.003   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 2258)
  covalent geometry    : angle       0.53331 ( 3091)
  SS BOND              : bond        0.00198 (    1)
  SS BOND              : angle       0.48873 (    2)
  hydrogen bonds       : bond        0.15697 (  160)
  hydrogen bonds       : angle       5.71552 (  474)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.1296
  time to fit residues: 4.0163
Evaluate side-chains
  23 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0060
   chunk 13 optimal weight:    0.0770
   chunk 1 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0870
   chunk 15 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 26 optimal weight:    0.3980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.2532

-------------------------------------------------------------------------------
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 = 0.3206 r_free = 0.3206 target = 0.116620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.101684 restraints weight = 2980.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.103936 restraints weight = 1761.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.105616 restraints weight = 1250.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.106719 restraints weight = 989.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.107438 restraints weight = 841.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3090
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3090
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.0897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   2259  Z= 0.104
  Angle     :  0.434   4.534   3093  Z= 0.238
  Chirality :  0.037   0.105    379
  Planarity :  0.003   0.028    368
  Dihedral  :  4.228  19.306    319
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 0.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  5.88 %
    Favored  : 92.31 %
  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:  2.54 (0.53), residues: 282
  helix:  2.14 (0.36), residues: 226
  sheet:  None (None), residues: 0
  loop : -0.14 (0.91), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 175 
 TYR   0.006   0.001   TYR R 209 
 PHE   0.006   0.001   PHE R 289 
 TRP   0.006   0.001   TRP R 158 
 HIS   0.007   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 2258)
  covalent geometry    : angle       0.43411 ( 3091)
  SS BOND              : bond        0.00297 (    1)
  SS BOND              : angle       0.20933 (    2)
  hydrogen bonds       : bond        0.03990 (  160)
  hydrogen bonds       : angle       4.04868 (  474)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.082 
Fit side-chains
  outliers start: 4
  outliers final: 2
  residues processed: 25
  average time/residue: 0.1121
  time to fit residues: 3.1755
Evaluate side-chains
  24 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 18 optimal weight:    0.4980
   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 = 0.3139 r_free = 0.3139 target = 0.112152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.097310 restraints weight = 3002.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.099584 restraints weight = 1808.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.101101 restraints weight = 1277.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.102167 restraints weight = 1020.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.102650 restraints weight = 868.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3024
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3024
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.0973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   2259  Z= 0.141
  Angle     :  0.462   4.662   3093  Z= 0.253
  Chirality :  0.038   0.102    379
  Planarity :  0.003   0.026    368
  Dihedral  :  4.306  19.176    319
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 0.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  9.95 %
    Favored  : 88.69 %
  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:  2.58 (0.53), residues: 282
  helix:  2.21 (0.36), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.33 (0.90), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 131 
 TYR   0.007   0.001   TYR R 132 
 PHE   0.008   0.001   PHE R 282 
 TRP   0.005   0.001   TRP R 158 
 HIS   0.007   0.002   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 2258)
  covalent geometry    : angle       0.46195 ( 3091)
  SS BOND              : bond        0.00432 (    1)
  SS BOND              : angle       0.31860 (    2)
  hydrogen bonds       : bond        0.04873 (  160)
  hydrogen bonds       : angle       3.99241 (  474)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 23
  time to evaluate  : 0.083 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 25
  average time/residue: 0.1108
  time to fit residues: 3.1435
Evaluate side-chains
  25 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  145 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 18 optimal weight:    0.4980
   chunk 0 optimal weight:    4.9990
   chunk 9 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0980
   chunk 12 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 20 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 = 0.3159 r_free = 0.3159 target = 0.113798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.098881 restraints weight = 2951.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.101167 restraints weight = 1763.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.102616 restraints weight = 1259.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.103669 restraints weight = 1013.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.104373 restraints weight = 871.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3045
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3045
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.1151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2259  Z= 0.114
  Angle     :  0.425   4.578   3093  Z= 0.232
  Chirality :  0.038   0.100    379
  Planarity :  0.003   0.026    368
  Dihedral  :  4.141  19.180    319
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 0.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 11.31 %
    Favored  : 85.97 %
  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:  2.65 (0.52), residues: 282
  helix:  2.29 (0.36), residues: 226
  sheet:  None (None), residues: 0
  loop : -0.51 (0.86), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 131 
 TYR   0.006   0.001   TYR R 209 
 PHE   0.006   0.001   PHE R 282 
 TRP   0.005   0.001   TRP R 158 
 HIS   0.006   0.002   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 2258)
  covalent geometry    : angle       0.42504 ( 3091)
  SS BOND              : bond        0.00337 (    1)
  SS BOND              : angle       0.30427 (    2)
  hydrogen bonds       : bond        0.04242 (  160)
  hydrogen bonds       : angle       3.86277 (  474)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 26
  time to evaluate  : 0.084 
Fit side-chains
REVERT: R   72 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.7965 (mp)
  outliers start: 6
  outliers final: 1
  residues processed: 29
  average time/residue: 0.1209
  time to fit residues: 3.9224
Evaluate side-chains
  25 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue  145 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0570
   chunk 23 optimal weight:    0.3980
   chunk 20 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.5498

-------------------------------------------------------------------------------
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 = 0.3159 r_free = 0.3159 target = 0.113347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.098430 restraints weight = 2953.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.100584 restraints weight = 1775.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.102112 restraints weight = 1291.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.103012 restraints weight = 1041.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.103752 restraints weight = 906.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3038
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3038
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.1210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   2259  Z= 0.125
  Angle     :  0.445   4.594   3093  Z= 0.242
  Chirality :  0.038   0.100    379
  Planarity :  0.003   0.025    368
  Dihedral  :  4.144  19.111    319
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 0.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 14.03 %
    Favored  : 84.16 %
  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:  2.59 (0.52), residues: 282
  helix:  2.32 (0.36), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.84 (0.81), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 239 
 TYR   0.006   0.001   TYR R 209 
 PHE   0.007   0.001   PHE R 282 
 TRP   0.005   0.001   TRP R 158 
 HIS   0.006   0.002   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 2258)
  covalent geometry    : angle       0.44508 ( 3091)
  SS BOND              : bond        0.00385 (    1)
  SS BOND              : angle       0.30935 (    2)
  hydrogen bonds       : bond        0.04438 (  160)
  hydrogen bonds       : angle       3.84934 (  474)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.090 
Fit side-chains
REVERT: R   72 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.7993 (mp)
  outliers start: 4
  outliers final: 2
  residues processed: 28
  average time/residue: 0.1299
  time to fit residues: 4.0539
Evaluate side-chains
  25 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 3 optimal weight:    0.0970
   chunk 13 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 10 optimal weight:    0.4980
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.5978

-------------------------------------------------------------------------------
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 = 0.3146 r_free = 0.3146 target = 0.112595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.097843 restraints weight = 2919.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.100080 restraints weight = 1758.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.101587 restraints weight = 1261.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.102488 restraints weight = 1017.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.102673 restraints weight = 882.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3025
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3025 r_free = 0.3025    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3025 r_free = 0.3025    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3025
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
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   0.039   2259  Z= 0.130
  Angle     :  0.444   4.601   3093  Z= 0.242
  Chirality :  0.038   0.101    379
  Planarity :  0.003   0.024    368
  Dihedral  :  4.162  19.065    319
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 1.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 15.38 %
    Favored  : 82.35 %
  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:  2.55 (0.52), residues: 282
  helix:  2.30 (0.36), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.86 (0.80), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 239 
 TYR   0.006   0.001   TYR R 209 
 PHE   0.007   0.001   PHE R 282 
 TRP   0.005   0.001   TRP R 158 
 HIS   0.006   0.002   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 2258)
  covalent geometry    : angle       0.44304 ( 3091)
  SS BOND              : bond        0.00096 (    1)
  SS BOND              : angle       1.33091 (    2)
  hydrogen bonds       : bond        0.04531 (  160)
  hydrogen bonds       : angle       3.86246 (  474)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.084 
Fit side-chains
REVERT: R   72 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.7982 (mp)
  outliers start: 5
  outliers final: 2
  residues processed: 27
  average time/residue: 0.1124
  time to fit residues: 3.4443
Evaluate side-chains
  25 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 18 optimal weight:    0.4980
   chunk 12 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 14 optimal weight:    0.2980
   chunk 2 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   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 = 0.3146 r_free = 0.3146 target = 0.112581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.097713 restraints weight = 2967.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.099861 restraints weight = 1781.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.101482 restraints weight = 1285.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.102465 restraints weight = 1026.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.103158 restraints weight = 883.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3032
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3032
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.1275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   2259  Z= 0.128
  Angle     :  0.452   4.590   3093  Z= 0.247
  Chirality :  0.038   0.101    379
  Planarity :  0.003   0.024    368
  Dihedral  :  4.134  19.074    319
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 1.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 14.93 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.55 (0.52), residues: 282
  helix:  2.30 (0.36), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.88 (0.79), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 239 
 TYR   0.006   0.001   TYR R 209 
 PHE   0.007   0.001   PHE R 282 
 TRP   0.005   0.001   TRP R 158 
 HIS   0.005   0.002   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 2258)
  covalent geometry    : angle       0.45186 ( 3091)
  SS BOND              : bond        0.00219 (    1)
  SS BOND              : angle       1.01026 (    2)
  hydrogen bonds       : bond        0.04501 (  160)
  hydrogen bonds       : angle       3.85191 (  474)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.094 
Fit side-chains
REVERT: R   72 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8051 (mp)
REVERT: R  113 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8183 (t0)
  outliers start: 5
  outliers final: 2
  residues processed: 27
  average time/residue: 0.1126
  time to fit residues: 3.4301
Evaluate side-chains
  27 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  113 ASP
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0570
   chunk 26 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.5898

-------------------------------------------------------------------------------
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 = 0.3145 r_free = 0.3145 target = 0.112405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.097592 restraints weight = 2955.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.099819 restraints weight = 1775.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.101231 restraints weight = 1275.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.102363 restraints weight = 1030.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.103060 restraints weight = 880.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3032
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3032
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
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   0.038   2259  Z= 0.128
  Angle     :  0.440   4.594   3093  Z= 0.240
  Chirality :  0.038   0.101    379
  Planarity :  0.003   0.024    368
  Dihedral  :  4.129  19.066    319
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 1.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 14.93 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.57 (0.52), residues: 282
  helix:  2.32 (0.36), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.87 (0.79), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 239 
 TYR   0.006   0.001   TYR R 209 
 PHE   0.007   0.001   PHE R 282 
 TRP   0.005   0.001   TRP R 158 
 HIS   0.005   0.002   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 2258)
  covalent geometry    : angle       0.43943 ( 3091)
  SS BOND              : bond        0.00217 (    1)
  SS BOND              : angle       0.85551 (    2)
  hydrogen bonds       : bond        0.04528 (  160)
  hydrogen bonds       : angle       3.84980 (  474)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 24
  time to evaluate  : 0.090 
Fit side-chains
REVERT: R   72 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.7981 (mp)
REVERT: R  113 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8190 (t0)
  outliers start: 5
  outliers final: 2
  residues processed: 27
  average time/residue: 0.1303
  time to fit residues: 3.9188
Evaluate side-chains
  28 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  113 ASP
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 24 optimal weight:    0.4980
   chunk 0 optimal weight:    4.9990
   chunk 5 optimal weight:    0.2980
   chunk 17 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 21 optimal weight:    0.2980
   chunk 16 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   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 = 0.3151 r_free = 0.3151 target = 0.112861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.097744 restraints weight = 3020.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.099990 restraints weight = 1813.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.101429 restraints weight = 1303.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.102494 restraints weight = 1052.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.103252 restraints weight = 906.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3029
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3029
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.1342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2259  Z= 0.126
  Angle     :  0.458   4.686   3093  Z= 0.249
  Chirality :  0.038   0.100    379
  Planarity :  0.003   0.024    368
  Dihedral  :  4.140  19.118    319
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 16.29 %
    Favored  : 81.90 %
  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:  2.58 (0.52), residues: 282
  helix:  2.35 (0.36), residues: 225
  sheet:  None (None), residues: 0
  loop : -1.02 (0.77), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 239 
 TYR   0.006   0.001   TYR R 209 
 PHE   0.007   0.001   PHE R 282 
 TRP   0.005   0.001   TRP R 158 
 HIS   0.005   0.002   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 2258)
  covalent geometry    : angle       0.45795 ( 3091)
  SS BOND              : bond        0.00232 (    1)
  SS BOND              : angle       0.76010 (    2)
  hydrogen bonds       : bond        0.04415 (  160)
  hydrogen bonds       : angle       3.82459 (  474)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 25
  time to evaluate  : 0.092 
Fit side-chains
REVERT: R   72 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8080 (mp)
REVERT: R  113 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8176 (t0)
  outliers start: 4
  outliers final: 2
  residues processed: 28
  average time/residue: 0.1237
  time to fit residues: 3.8971
Evaluate side-chains
  27 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  113 ASP
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 21 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 15 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   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 = 0.3119 r_free = 0.3119 target = 0.110448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.095597 restraints weight = 3001.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.097652 restraints weight = 1805.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.099297 restraints weight = 1307.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.100251 restraints weight = 1040.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.100700 restraints weight = 897.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2999
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2999 r_free = 0.2999    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2999 r_free = 0.2999    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2999
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.1368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   2259  Z= 0.159
  Angle     :  0.472   4.648   3093  Z= 0.258
  Chirality :  0.039   0.104    379
  Planarity :  0.003   0.024    368
  Dihedral  :  4.265  18.927    319
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 1.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 17.19 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.41 (0.52), residues: 282
  helix:  2.24 (0.36), residues: 225
  sheet:  None (None), residues: 0
  loop : -1.12 (0.76), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 328 
 TYR   0.006   0.001   TYR R 132 
 PHE   0.008   0.001   PHE R 282 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.006   0.002   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 2258)
  covalent geometry    : angle       0.47108 ( 3091)
  SS BOND              : bond        0.00301 (    1)
  SS BOND              : angle       0.91830 (    2)
  hydrogen bonds       : bond        0.05085 (  160)
  hydrogen bonds       : angle       3.94482 (  474)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 25
  time to evaluate  : 0.083 
Fit side-chains
REVERT: R   72 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.7997 (mp)
REVERT: R  113 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8246 (t0)
  outliers start: 4
  outliers final: 2
  residues processed: 29
  average time/residue: 0.1218
  time to fit residues: 3.9354
Evaluate side-chains
  27 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  113 ASP
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 11 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 5 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3125 r_free = 0.3125 target = 0.110996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.095924 restraints weight = 3035.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.098097 restraints weight = 1829.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.099602 restraints weight = 1315.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.100697 restraints weight = 1051.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.101371 restraints weight = 899.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3009
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3009 r_free = 0.3009    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3009 r_free = 0.3009    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3009
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.1375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   2259  Z= 0.153
  Angle     :  0.489   5.190   3093  Z= 0.267
  Chirality :  0.039   0.109    379
  Planarity :  0.003   0.024    368
  Dihedral  :  4.296  19.048    319
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 16.29 %
    Favored  : 81.90 %
  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:  2.34 (0.51), residues: 282
  helix:  2.23 (0.36), residues: 224
  sheet:  None (None), residues: 0
  loop : -1.27 (0.75), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 304 
 TYR   0.006   0.001   TYR R 308 
 PHE   0.008   0.001   PHE R 282 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.006   0.002   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 2258)
  covalent geometry    : angle       0.48902 ( 3091)
  SS BOND              : bond        0.00308 (    1)
  SS BOND              : angle       0.88315 (    2)
  hydrogen bonds       : bond        0.04937 (  160)
  hydrogen bonds       : angle       3.94034 (  474)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 697.22 seconds
wall clock time: 12 minutes 29.92 seconds (749.92 seconds total)