Starting phenix.real_space_refine
on Fri Aug 22 12:40:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggk_40011/08_2025/8ggk_40011.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggk_40011/08_2025/8ggk_40011.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ggk_40011/08_2025/8ggk_40011.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggk_40011/08_2025/8ggk_40011.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggk_40011/08_2025/8ggk_40011.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggk_40011/08_2025/8ggk_40011.cif"
  }
  resolution = 3.3
  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=   0.028
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      16      5.16       5
     C    1479      2.51       5
     N     353      2.21       5
     O     370      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: 2218
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2201
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2201
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 7, 'TRANS': 280}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 121
          Unresolved non-hydrogen angles: 149
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 8, 'TRP:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 82
    Chain: "R"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 17
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1, 'water': 2}
          Link IDs: {None: 2}
  Time building chain proxies: 0.84, per 1000 atoms: 0.38
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (59.0036, 86.77, 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      16     16.00
     O     370      8.00
     N     353      7.00
     C    1479      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: 0.23
  Conformation dependent library (CDL) restraints added in 97.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  552

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 0 sheets defined
      87.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'R' and resid 30 through 61
      removed outlier: 3.680A  pdb=" N   MET R  36 " --> pdb=" O   TRP R  32 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   GLY R  37 " --> pdb=" O   VAL R  33 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 4.553A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 3.768A  pdb=" N   CYS R 106 " --> pdb=" O   GLY R 102 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   GLU R 107 " --> pdb=" O   ASN R 103 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 148 through 166
      removed outlier: 3.687A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ILE R 154 " --> pdb=" O   ALA R 150 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   SER R 165 " --> pdb=" O   SER R 161 " (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
    Processing helix  chain 'R' and resid 282 through 287
    Processing helix  chain 'R' and resid 288 through 299
      removed outlier: 3.545A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ILE R 298 " --> pdb=" O   ILE R 294 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.691A  pdb=" N   TYR R 308 " --> pdb=" O   ARG R 304 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ILE R 309 " --> pdb=" O   LYS R 305 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 318 through 320
      No H-bonds generated for 'chain 'R' and resid 318 through 320'
    Processing helix  chain 'R' and resid 321 through 327
    Processing helix  chain 'R' and resid 329 through 340

    166 hydrogen bonds defined for protein.
    498 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.31

  Time building geometry restraints manager: 0.29 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 660
        1.35 -     1.46: 608
        1.46 -     1.58: 984
        1.58 -     1.70: 0
        1.70 -     1.82: 22
  Bond restraints: 2274
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.448 -0.051 2.00e-02 2.50e+03 6.39e+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 4.70e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.436 -0.042 2.00e-02 2.50e+03 4.46e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.559 -0.039 2.00e-02 2.50e+03 3.87e+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 2.90e+00
  ... (remaining 2269 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.11: 2985
        1.11 -     2.22: 100
        2.22 -     3.33: 15
        3.33 -     4.44: 7
        4.44 -     5.55: 7
  Bond angle restraints: 3114
  Sorted by residual:
  angle pdb=" C   HIS R 241 "
        pdb=" N   VAL R 242 "
        pdb=" CA  VAL R 242 "
      ideal   model   delta    sigma   weight residual
     121.70  125.97   -4.27 1.80e+00 3.09e-01 5.64e+00
  angle pdb=" N   VAL R  87 "
        pdb=" CA  VAL R  87 "
        pdb=" C   VAL R  87 "
      ideal   model   delta    sigma   weight residual
     108.88  112.82   -3.94 2.16e+00 2.14e-01 3.33e+00
  angle pdb=" N   SER R 207 "
        pdb=" CA  SER R 207 "
        pdb=" C   SER R 207 "
      ideal   model   delta    sigma   weight residual
     111.69  113.86   -2.17 1.23e+00 6.61e-01 3.11e+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  117.69   -5.06 3.00e+00 1.11e-01 2.84e+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  127.11   -2.80 1.67e+00 3.59e-01 2.80e+00
  ... (remaining 3109 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.74: 1081
       10.74 -    21.47: 139
       21.47 -    32.20: 55
       32.20 -    42.93: 23
       42.93 -    53.67: 5
  Dihedral angle restraints: 1303
    sinusoidal: 454
      harmonic: 849
  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 -159.29  -20.71     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  HIS R 178 "
           pdb=" C   HIS R 178 "
           pdb=" N   GLN R 179 "
           pdb=" CA  GLN R 179 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.07  -16.93     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" CG  ARG R 328 "
           pdb=" CD  ARG R 328 "
           pdb=" NE  ARG R 328 "
           pdb=" CZ  ARG R 328 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  136.83   43.17     2      1.50e+01 4.44e-03 9.99e+00
  ... (remaining 1300 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 214
       0.030 -    0.060: 117
       0.060 -    0.090: 36
       0.090 -    0.120: 14
       0.120 -    0.151: 1
  Chirality restraints: 382
  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 5.67e-01
  chirality pdb=" CA  LEU R 287 "
            pdb=" N   LEU R 287 "
            pdb=" C   LEU R 287 "
            pdb=" CB  LEU R 287 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 2.80e-01
  chirality pdb=" CA  ASN R 322 "
            pdb=" N   ASN R 322 "
            pdb=" C   ASN R 322 "
            pdb=" CB  ASN R 322 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.41    0.10 2.00e-01 2.50e+01 2.60e-01
  ... (remaining 379 not shown)

  Planarity restraints: 372
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 322 "    0.014 5.00e-02 4.00e+02   2.05e-02 6.74e-01
        pdb=" N   PRO R 323 "   -0.035 5.00e-02 4.00e+02
        pdb=" CA  PRO R 323 "    0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO R 323 "    0.012 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 210 "    0.013 5.00e-02 4.00e+02   1.97e-02 6.23e-01
        pdb=" N   PRO R 211 "   -0.034 5.00e-02 4.00e+02
        pdb=" CA  PRO R 211 "    0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO R 211 "    0.011 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 167 "   -0.013 5.00e-02 4.00e+02   1.93e-02 5.95e-01
        pdb=" N   PRO R 168 "    0.033 5.00e-02 4.00e+02
        pdb=" CA  PRO R 168 "   -0.009 5.00e-02 4.00e+02
        pdb=" CD  PRO R 168 "   -0.011 5.00e-02 4.00e+02
  ... (remaining 369 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 512
        2.79 -     3.32: 2157
        3.32 -     3.84: 3513
        3.84 -     4.37: 3734
        4.37 -     4.90: 6864
  Nonbonded interactions: 16780
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAL G1I R 501 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OH  TYR R 174 "
            pdb=" O   HOH R 601 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   SER R 111 "
            pdb=" OG  SER R 165 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" O   LEU R  64 "
            pdb=" ND2 ASN R  69 "
     model   vdw
     2.401 3.120
  nonbonded pdb=" N   HIS R 178 "
            pdb=" O   HIS R 178 "
     model   vdw
     2.641 2.496
  ... (remaining 16775 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.460
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.640
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   2275  Z= 0.205
  Angle     :  0.550   5.548   3116  Z= 0.299
  Chirality :  0.040   0.151    382
  Planarity :  0.003   0.021    372
  Dihedral  : 12.874  53.666    748
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  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:  1.77 (0.52), residues: 284
  helix:  2.00 (0.36), residues: 211
  sheet:  None (None), residues: 0
  loop : -1.34 (0.75), residues: 73

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 131 
 TYR   0.008   0.001   TYR R 209 
 PHE   0.009   0.001   PHE R 104 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 2274)
  covalent geometry    : angle       0.54954 ( 3114)
  SS BOND              : bond        0.00084 (    1)
  SS BOND              : angle       1.30825 (    2)
  hydrogen bonds       : bond        0.15685 (  166)
  hydrogen bonds       : angle       5.96689 (  498)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.114 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.1140
  time to fit residues: 3.4928
Evaluate side-chains
  22 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 12 optimal weight:    0.3980
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   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 = 0.3207 r_free = 0.3207 target = 0.115387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.100836 restraints weight = 3046.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 1.69
r_work: 0.2915 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2802 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2796
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2796 r_free = 0.2796    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2796 r_free = 0.2796    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2796
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.0715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2275  Z= 0.161
  Angle     :  0.511   5.596   3116  Z= 0.284
  Chirality :  0.039   0.109    382
  Planarity :  0.003   0.023    372
  Dihedral  :  4.436  21.104    320
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  :  5.78 %
    Favored  : 92.00 %
  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:  1.86 (0.51), residues: 284
  helix:  1.99 (0.35), residues: 219
  sheet:  None (None), residues: 0
  loop : -1.45 (0.79), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 221 
 TYR   0.007   0.001   TYR R 308 
 PHE   0.009   0.001   PHE R  61 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 2274)
  covalent geometry    : angle       0.51080 ( 3114)
  SS BOND              : bond        0.00060 (    1)
  SS BOND              : angle       1.09394 (    2)
  hydrogen bonds       : bond        0.07028 (  166)
  hydrogen bonds       : angle       4.55274 (  498)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.086 
Fit side-chains
  outliers start: 5
  outliers final: 3
  residues processed: 25
  average time/residue: 0.0980
  time to fit residues: 2.8168
Evaluate side-chains
  24 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   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 = 0.3197 r_free = 0.3197 target = 0.114941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.100134 restraints weight = 3083.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 1.71
r_work: 0.2907 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2792 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2783
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2783 r_free = 0.2783    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2783 r_free = 0.2783    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2783
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.0875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2275  Z= 0.156
  Angle     :  0.499   5.484   3116  Z= 0.276
  Chirality :  0.039   0.105    382
  Planarity :  0.003   0.023    372
  Dihedral  :  4.434  20.982    320
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  :  9.33 %
    Favored  : 88.00 %
  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:  1.89 (0.51), residues: 284
  helix:  1.98 (0.35), residues: 220
  sheet:  None (None), residues: 0
  loop : -1.36 (0.80), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 221 
 TYR   0.007   0.001   TYR R 209 
 PHE   0.008   0.001   PHE R  61 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 2274)
  covalent geometry    : angle       0.49865 ( 3114)
  SS BOND              : bond        0.00073 (    1)
  SS BOND              : angle       1.10836 (    2)
  hydrogen bonds       : bond        0.06784 (  166)
  hydrogen bonds       : angle       4.38288 (  498)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 20
  time to evaluate  : 0.094 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 24
  average time/residue: 0.0990
  time to fit residues: 2.7424
Evaluate side-chains
  24 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 20
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3181 r_free = 0.3181 target = 0.113809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.099417 restraints weight = 3045.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 1.61
r_work: 0.2894 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2784 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2776
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2776 r_free = 0.2776    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2776 r_free = 0.2776    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2776
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.0993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   2275  Z= 0.165
  Angle     :  0.505   5.518   3116  Z= 0.279
  Chirality :  0.039   0.104    382
  Planarity :  0.003   0.024    372
  Dihedral  :  4.453  20.962    320
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 1.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 11.11 %
    Favored  : 87.11 %
  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:  1.89 (0.52), residues: 284
  helix:  2.01 (0.35), residues: 219
  sheet:  None (None), residues: 0
  loop : -1.44 (0.79), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 221 
 TYR   0.007   0.001   TYR R 209 
 PHE   0.008   0.001   PHE R  61 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 2274)
  covalent geometry    : angle       0.50404 ( 3114)
  SS BOND              : bond        0.00095 (    1)
  SS BOND              : angle       1.13935 (    2)
  hydrogen bonds       : bond        0.06962 (  166)
  hydrogen bonds       : angle       4.35365 (  498)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.088 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 25
  average time/residue: 0.0732
  time to fit residues: 2.1922
Evaluate side-chains
  23 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   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 = 0.3191 r_free = 0.3191 target = 0.114602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.099773 restraints weight = 3052.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 1.71
r_work: 0.2900 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2788 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2778
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2778 r_free = 0.2778    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2778 r_free = 0.2778    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2778
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.1080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2275  Z= 0.152
  Angle     :  0.489   5.499   3116  Z= 0.270
  Chirality :  0.038   0.102    382
  Planarity :  0.003   0.024    372
  Dihedral  :  4.378  20.962    320
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 1.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 11.11 %
    Favored  : 85.78 %
  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:  1.98 (0.52), residues: 284
  helix:  2.08 (0.36), residues: 219
  sheet:  None (None), residues: 0
  loop : -1.46 (0.78), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 221 
 TYR   0.007   0.001   TYR R 209 
 PHE   0.008   0.001   PHE R  61 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 2274)
  covalent geometry    : angle       0.48856 ( 3114)
  SS BOND              : bond        0.00114 (    1)
  SS BOND              : angle       1.11521 (    2)
  hydrogen bonds       : bond        0.06635 (  166)
  hydrogen bonds       : angle       4.28003 (  498)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 21
  time to evaluate  : 0.082 
Fit side-chains
  outliers start: 7
  outliers final: 6
  residues processed: 27
  average time/residue: 0.0918
  time to fit residues: 2.8308
Evaluate side-chains
  27 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 21
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0170
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.5618

-------------------------------------------------------------------------------
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 = 0.3209 r_free = 0.3209 target = 0.115876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.101206 restraints weight = 3036.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 1.67
r_work: 0.2921 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2808 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2801
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2801 r_free = 0.2801    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2801 r_free = 0.2801    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2801
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.1172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2275  Z= 0.140
  Angle     :  0.483   5.453   3116  Z= 0.266
  Chirality :  0.038   0.102    382
  Planarity :  0.003   0.023    372
  Dihedral  :  4.299  20.913    320
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 12.44 %
    Favored  : 84.89 %
  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:  2.05 (0.51), residues: 284
  helix:  2.14 (0.35), residues: 219
  sheet:  None (None), residues: 0
  loop : -1.43 (0.77), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 221 
 TYR   0.007   0.001   TYR R 209 
 PHE   0.008   0.001   PHE R  61 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 2274)
  covalent geometry    : angle       0.48197 ( 3114)
  SS BOND              : bond        0.00116 (    1)
  SS BOND              : angle       1.11158 (    2)
  hydrogen bonds       : bond        0.06298 (  166)
  hydrogen bonds       : angle       4.18954 (  498)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.102 
Fit side-chains
  outliers start: 6
  outliers final: 5
  residues processed: 28
  average time/residue: 0.0870
  time to fit residues: 2.8241
Evaluate side-chains
  28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 23
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 6 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 21 optimal weight:    0.1980
   chunk 8 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 27 optimal weight:    0.5980
   chunk 2 optimal weight:    0.1980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.3980

-------------------------------------------------------------------------------
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 = 0.3252 r_free = 0.3252 target = 0.119392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.104798 restraints weight = 3004.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 1.66
r_work: 0.2969 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2849
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2849 r_free = 0.2849    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2849 r_free = 0.2849    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2849
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.1344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2275  Z= 0.122
  Angle     :  0.461   5.414   3116  Z= 0.253
  Chirality :  0.037   0.104    382
  Planarity :  0.003   0.023    372
  Dihedral  :  4.142  20.754    320
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 12.00 %
    Favored  : 84.89 %
  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:  2.25 (0.51), residues: 284
  helix:  2.27 (0.35), residues: 220
  sheet:  None (None), residues: 0
  loop : -1.38 (0.77), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 221 
 TYR   0.006   0.001   TYR R 209 
 PHE   0.007   0.001   PHE R 104 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 2274)
  covalent geometry    : angle       0.45994 ( 3114)
  SS BOND              : bond        0.00081 (    1)
  SS BOND              : angle       1.05780 (    2)
  hydrogen bonds       : bond        0.05460 (  166)
  hydrogen bonds       : angle       4.03528 (  498)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 26
  time to evaluate  : 0.078 
Fit side-chains
REVERT: R  227 LYS cc_start: 0.8025 (tttt) cc_final: 0.7669 (ttmm)
REVERT: R  231 GLN cc_start: 0.7948 (tt0) cc_final: 0.7730 (tm-30)
  outliers start: 7
  outliers final: 6
  residues processed: 32
  average time/residue: 0.0806
  time to fit residues: 3.0021
Evaluate side-chains
  32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 26
  time to evaluate  : 0.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3174 r_free = 0.3174 target = 0.112700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.097990 restraints weight = 3071.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 1.66
r_work: 0.2881 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2769 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2761
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2761 r_free = 0.2761    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2761 r_free = 0.2761    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2761
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.1283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2275  Z= 0.179
  Angle     :  0.518   5.505   3116  Z= 0.287
  Chirality :  0.040   0.107    382
  Planarity :  0.003   0.030    372
  Dihedral  :  4.424  20.735    320
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 12.89 %
    Favored  : 84.44 %
  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:  1.91 (0.51), residues: 284
  helix:  2.05 (0.35), residues: 219
  sheet:  None (None), residues: 0
  loop : -1.56 (0.74), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 175 
 TYR   0.007   0.001   TYR R 209 
 PHE   0.010   0.001   PHE R  61 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.002   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 2274)
  covalent geometry    : angle       0.51712 ( 3114)
  SS BOND              : bond        0.00169 (    1)
  SS BOND              : angle       1.22723 (    2)
  hydrogen bonds       : bond        0.07165 (  166)
  hydrogen bonds       : angle       4.28762 (  498)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.097 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 28
  average time/residue: 0.0779
  time to fit residues: 2.5877
Evaluate side-chains
  28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 2 optimal weight:    0.4980
   chunk 24 optimal weight:    0.2980
   chunk 10 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0670
   chunk 25 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.4718

-------------------------------------------------------------------------------
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 = 0.3226 r_free = 0.3226 target = 0.116932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.102174 restraints weight = 3066.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3041 rms_B_bonded: 1.68
r_work: 0.2940 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2826 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2817
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2817 r_free = 0.2817    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2817 r_free = 0.2817    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2817
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
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      :  0.003   0.028   2275  Z= 0.129
  Angle     :  0.468   5.452   3116  Z= 0.258
  Chirality :  0.038   0.106    382
  Planarity :  0.003   0.023    372
  Dihedral  :  4.200  20.988    320
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 12.89 %
    Favored  : 84.44 %
  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:  2.13 (0.51), residues: 284
  helix:  2.17 (0.35), residues: 220
  sheet:  None (None), residues: 0
  loop : -1.36 (0.78), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 221 
 TYR   0.006   0.001   TYR R 209 
 PHE   0.007   0.001   PHE R 104 
 TRP   0.006   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 2274)
  covalent geometry    : angle       0.46710 ( 3114)
  SS BOND              : bond        0.00100 (    1)
  SS BOND              : angle       1.04652 (    2)
  hydrogen bonds       : bond        0.05897 (  166)
  hydrogen bonds       : angle       4.08586 (  498)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 25
  time to evaluate  : 0.117 
Fit side-chains
REVERT: R  227 LYS cc_start: 0.8044 (tttt) cc_final: 0.7687 (ttmm)
REVERT: R  231 GLN cc_start: 0.7999 (tt0) cc_final: 0.7756 (tm-30)
  outliers start: 6
  outliers final: 6
  residues processed: 30
  average time/residue: 0.1037
  time to fit residues: 3.5551
Evaluate side-chains
  30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 24
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 27 optimal weight:    0.0270
   chunk 7 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.7038

-------------------------------------------------------------------------------
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 = 0.3197 r_free = 0.3197 target = 0.114531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.099723 restraints weight = 3071.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 1.68
r_work: 0.2905 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2790 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2781
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2781 r_free = 0.2781    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2781 r_free = 0.2781    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2781
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.1338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   2275  Z= 0.155
  Angle     :  0.490   5.465   3116  Z= 0.271
  Chirality :  0.039   0.106    382
  Planarity :  0.003   0.023    372
  Dihedral  :  4.295  20.747    320
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 1.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 12.89 %
    Favored  : 84.44 %
  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:  2.03 (0.51), residues: 284
  helix:  2.13 (0.35), residues: 219
  sheet:  None (None), residues: 0
  loop : -1.49 (0.77), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 221 
 TYR   0.007   0.001   TYR R 209 
 PHE   0.008   0.001   PHE R  61 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 2274)
  covalent geometry    : angle       0.48940 ( 3114)
  SS BOND              : bond        0.00146 (    1)
  SS BOND              : angle       1.13946 (    2)
  hydrogen bonds       : bond        0.06583 (  166)
  hydrogen bonds       : angle       4.15970 (  498)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 20
  time to evaluate  : 0.068 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 25
  average time/residue: 0.0544
  time to fit residues: 1.6843
Evaluate side-chains
  26 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 20
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 23 optimal weight:    0.4980
   chunk 15 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   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 = 0.3197 r_free = 0.3197 target = 0.114573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.099732 restraints weight = 3084.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 1.69
r_work: 0.2905 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2793 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2788
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2788 r_free = 0.2788    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2787 r_free = 0.2787    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2787
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.1351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2275  Z= 0.151
  Angle     :  0.487   5.473   3116  Z= 0.269
  Chirality :  0.039   0.106    382
  Planarity :  0.003   0.023    372
  Dihedral  :  4.288  20.840    320
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 1.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 12.89 %
    Favored  : 84.44 %
  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:  2.03 (0.51), residues: 284
  helix:  2.13 (0.35), residues: 219
  sheet:  None (None), residues: 0
  loop : -1.48 (0.77), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 221 
 TYR   0.007   0.001   TYR R 209 
 PHE   0.008   0.001   PHE R  61 
 TRP   0.006   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 2274)
  covalent geometry    : angle       0.48630 ( 3114)
  SS BOND              : bond        0.00125 (    1)
  SS BOND              : angle       1.12077 (    2)
  hydrogen bonds       : bond        0.06564 (  166)
  hydrogen bonds       : angle       4.16006 (  498)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 839.79 seconds
wall clock time: 14 minutes 53.28 seconds (893.28 seconds total)