Starting phenix.real_space_refine
on Fri Aug 22 12:38:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggm_40013/08_2025/8ggm_40013.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggm_40013/08_2025/8ggm_40013.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggm_40013/08_2025/8ggm_40013.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggm_40013/08_2025/8ggm_40013.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ggm_40013/08_2025/8ggm_40013.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggm_40013/08_2025/8ggm_40013.map"
  }
  resolution = 3.2
  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=   0.029
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    1473      2.51       5
     N     352      2.21       5
     O     371      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  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: 2211
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2196
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2196
          Classifications: {'peptide': 287}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 7, 'TRANS': 279}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 119
          Unresolved non-hydrogen angles: 146
          Unresolved non-hydrogen dihedrals: 99
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 6, 'TRP:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 70
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.84, per 1000 atoms: 0.38
  Number of scatterers: 2211
  At special positions: 0
  Unit cell: (59.0036, 87.6377, 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     371      8.00
     N     352      7.00
     C    1473      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: 0.28
  Conformation dependent library (CDL) restraints added in 53.8 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  550

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 0 sheets defined
      87.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'R' and resid 31 through 61
      removed outlier: 3.881A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 4.171A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 140 through 145
      removed outlier: 3.614A  pdb=" N   LEU R 145 " --> pdb=" O   TYR R 141 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.892A  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)
      removed outlier: 3.513A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
      removed outlier: 3.528A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 186
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 238
    Processing helix  chain 'R' and resid 269 through 299
      removed outlier: 4.219A  pdb=" N   THR R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.589A  pdb=" N   ILE R 291 " --> pdb=" O   LEU R 287 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.607A  pdb=" N   GLY R 315 " --> pdb=" O   LEU R 311 " (cutoff:3.500A)
      removed outlier: 3.757A  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

    173 hydrogen bonds defined for protein.
    519 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: 0.32 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: 664
        1.35 -     1.46: 607
        1.46 -     1.58: 978
        1.58 -     1.70: 0
        1.70 -     1.81: 21
  Bond restraints: 2270
  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 6.82e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.441 -0.047 2.00e-02 2.50e+03 5.58e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.568 -0.045 2.00e-02 2.50e+03 5.17e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.560 -0.040 2.00e-02 2.50e+03 4.03e+00
  bond pdb=" CAE G1I R 501 "
       pdb=" CAG G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.506  1.540 -0.034 2.00e-02 2.50e+03 2.89e+00
  ... (remaining 2265 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 3004
        1.23 -     2.45: 79
        2.45 -     3.68: 15
        3.68 -     4.91: 8
        4.91 -     6.14: 3
  Bond angle restraints: 3109
  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  125.51   -3.81 1.80e+00 3.09e-01 4.48e+00
  angle pdb=" C   LEU R  84 "
        pdb=" N   ALA R  85 "
        pdb=" CA  ALA R  85 "
      ideal   model   delta    sigma   weight residual
     122.42  119.35    3.07 1.55e+00 4.16e-01 3.93e+00
  angle pdb=" C   CYS R 285 "
        pdb=" N   TRP R 286 "
        pdb=" CA  TRP R 286 "
      ideal   model   delta    sigma   weight residual
     122.11  119.06    3.05 1.64e+00 3.72e-01 3.45e+00
  angle pdb=" CG  ARG R  63 "
        pdb=" CD  ARG R  63 "
        pdb=" NE  ARG R  63 "
      ideal   model   delta    sigma   weight residual
     112.00  116.00   -4.00 2.20e+00 2.07e-01 3.31e+00
  angle pdb=" CA  LEU R 144 "
        pdb=" CB  LEU R 144 "
        pdb=" CG  LEU R 144 "
      ideal   model   delta    sigma   weight residual
     116.30  122.44   -6.14 3.50e+00 8.16e-02 3.07e+00
  ... (remaining 3104 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.67: 1177
       16.67 -    33.33: 99
       33.33 -    50.00: 17
       50.00 -    66.67: 2
       66.67 -    83.33: 3
  Dihedral angle restraints: 1298
    sinusoidal: 452
      harmonic: 846
  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 -158.00  -22.00     0      5.00e+00 4.00e-02 1.94e+01
  dihedral pdb=" CA  ASN R  51 "
           pdb=" CB  ASN R  51 "
           pdb=" CG  ASN R  51 "
           pdb=" OD1 ASN R  51 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -161.22   71.22     2      2.00e+01 2.50e-03 1.08e+01
  dihedral pdb=" CA  ALA R  85 "
           pdb=" C   ALA R  85 "
           pdb=" N   VAL R  86 "
           pdb=" CA  VAL R  86 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.07  -15.93     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 1295 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 238
       0.029 -    0.058: 87
       0.058 -    0.087: 40
       0.087 -    0.117: 12
       0.117 -    0.146: 1
  Chirality restraints: 378
  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    2.54   -0.15 2.00e-01 2.50e+01 5.31e-01
  chirality pdb=" CA  TRP R 286 "
            pdb=" N   TRP R 286 "
            pdb=" C   TRP R 286 "
            pdb=" CB  TRP R 286 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 3.12e-01
  chirality pdb=" CA  PRO R 138 "
            pdb=" N   PRO R 138 "
            pdb=" C   PRO R 138 "
            pdb=" CB  PRO R 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 3.02e-01
  ... (remaining 375 not shown)

  Planarity restraints: 374
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 167 "   -0.019 5.00e-02 4.00e+02   2.91e-02 1.36e+00
        pdb=" N   PRO R 168 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO R 168 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO R 168 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 287 "   -0.018 5.00e-02 4.00e+02   2.73e-02 1.19e+00
        pdb=" N   PRO R 288 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO R 288 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO R 288 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 322 "    0.018 5.00e-02 4.00e+02   2.67e-02 1.14e+00
        pdb=" N   PRO R 323 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO R 323 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO R 323 "    0.015 5.00e-02 4.00e+02
  ... (remaining 371 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 613
        2.82 -     3.34: 2174
        3.34 -     3.86: 3515
        3.86 -     4.38: 3713
        4.38 -     4.90: 6868
  Nonbonded interactions: 16883
  Sorted by model distance:
  nonbonded pdb=" O   SER R 111 "
            pdb=" OG  SER R 165 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAL G1I R 501 "
     model   vdw
     2.384 3.040
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAK G1I R 501 "
     model   vdw
     2.444 3.040
  nonbonded pdb=" N   GLU R 306 "
            pdb=" OE1 GLU R 306 "
     model   vdw
     2.547 3.120
  nonbonded pdb=" O   ASN R  69 "
            pdb=" OG1 THR R  73 "
     model   vdw
     2.591 3.040
  ... (remaining 16878 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:             2.400
  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:             0.020
  Extract box with map and model:          0.020
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.160
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
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   2271  Z= 0.179
  Angle     :  0.540   6.137   3111  Z= 0.294
  Chirality :  0.038   0.146    378
  Planarity :  0.004   0.035    374
  Dihedral  : 13.214  83.331    745
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 2.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.21 (0.51), residues: 283
  helix:  2.23 (0.35), residues: 214
  sheet:  None (None), residues: 0
  loop : -1.06 (0.75), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG R  63 
 TYR   0.007   0.001   TYR R 199 
 PHE   0.009   0.001   PHE R 290 
 TRP   0.007   0.001   TRP R 109 
 HIS   0.002   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 2270)
  covalent geometry    : angle       0.53989 ( 3109)
  SS BOND              : bond        0.00120 (    1)
  SS BOND              : angle       1.14605 (    2)
  hydrogen bonds       : bond        0.16387 (  173)
  hydrogen bonds       : angle       5.75280 (  519)

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

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

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.090 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.1746
  time to fit residues: 4.2151
Evaluate side-chains
  20 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
R  51 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.116300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.093829 restraints weight = 2814.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.2926 rms_B_bonded: 1.65
r_work: 0.2811 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2686 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2680
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2680 r_free = 0.2680    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2680 r_free = 0.2680    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2680
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.0906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2271  Z= 0.151
  Angle     :  0.507   6.741   3111  Z= 0.281
  Chirality :  0.040   0.127    378
  Planarity :  0.004   0.029    374
  Dihedral  :  4.493  22.669    319
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 1.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  8.97 %
    Favored  : 90.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.11 (0.50), residues: 283
  helix:  2.00 (0.35), residues: 226
  sheet:  None (None), residues: 0
  loop : -1.07 (0.74), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG R  63 
 TYR   0.007   0.001   TYR R 199 
 PHE   0.011   0.001   PHE R 290 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 2270)
  covalent geometry    : angle       0.50604 ( 3109)
  SS BOND              : bond        0.00130 (    1)
  SS BOND              : angle       1.03883 (    2)
  hydrogen bonds       : bond        0.06885 (  173)
  hydrogen bonds       : angle       4.49399 (  519)

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

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

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.106 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 23
  average time/residue: 0.1166
  time to fit residues: 3.0379
Evaluate side-chains
  21 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 2 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0770
   chunk 13 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.116854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.094249 restraints weight = 2841.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.2932 rms_B_bonded: 1.65
r_work: 0.2819 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2696 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2690
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2690 r_free = 0.2690    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2690 r_free = 0.2690    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2690
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.1085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2271  Z= 0.137
  Angle     :  0.474   5.182   3111  Z= 0.264
  Chirality :  0.039   0.127    378
  Planarity :  0.004   0.027    374
  Dihedral  :  4.422  22.629    319
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  9.42 %
    Favored  : 89.24 %
  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 (0.50), residues: 283
  helix:  2.10 (0.34), residues: 226
  sheet:  None (None), residues: 0
  loop : -1.03 (0.74), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R  63 
 TYR   0.007   0.001   TYR R 199 
 PHE   0.010   0.001   PHE R 290 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 2270)
  covalent geometry    : angle       0.47352 ( 3109)
  SS BOND              : bond        0.00140 (    1)
  SS BOND              : angle       0.99186 (    2)
  hydrogen bonds       : bond        0.06387 (  173)
  hydrogen bonds       : angle       4.25980 (  519)

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

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

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.098 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 24
  average time/residue: 0.1104
  time to fit residues: 3.0059
Evaluate side-chains
  22 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 21
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 14 optimal weight:    0.3980
   chunk 3 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0870
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.118634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.096146 restraints weight = 2847.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 1.65
r_work: 0.2846 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2723 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2716
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2716
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.1198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2271  Z= 0.123
  Angle     :  0.469   8.163   3111  Z= 0.252
  Chirality :  0.038   0.125    378
  Planarity :  0.003   0.026    374
  Dihedral  :  4.274  22.530    319
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 1.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 11.21 %
    Favored  : 87.89 %
  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:  2.60 (0.50), residues: 283
  helix:  2.26 (0.34), residues: 230
  sheet:  None (None), residues: 0
  loop : -0.75 (0.80), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 151 
 TYR   0.006   0.001   TYR R 199 
 PHE   0.009   0.001   PHE R 290 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 2270)
  covalent geometry    : angle       0.46862 ( 3109)
  SS BOND              : bond        0.00112 (    1)
  SS BOND              : angle       0.94611 (    2)
  hydrogen bonds       : bond        0.05803 (  173)
  hydrogen bonds       : angle       4.08989 (  519)

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

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

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.104 
Fit side-chains
REVERT: R   36 MET cc_start: 0.7126 (mtm) cc_final: 0.6868 (mtt)
  outliers start: 2
  outliers final: 1
  residues processed: 26
  average time/residue: 0.1128
  time to fit residues: 3.3124
Evaluate side-chains
  23 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9980
   chunk 13 optimal weight:    0.3980
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.114882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.093109 restraints weight = 2830.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.2924 rms_B_bonded: 1.55
r_work: 0.2810 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2686 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2678
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2678 r_free = 0.2678    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2678 r_free = 0.2678    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2678
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.1287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2271  Z= 0.148
  Angle     :  0.494   8.218   3111  Z= 0.268
  Chirality :  0.039   0.127    378
  Planarity :  0.003   0.027    374
  Dihedral  :  4.363  22.677    319
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 2.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 13.45 %
    Favored  : 85.20 %
  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 (0.50), residues: 283
  helix:  2.21 (0.34), residues: 230
  sheet:  None (None), residues: 0
  loop : -0.66 (0.82), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 131 
 TYR   0.007   0.001   TYR R 199 
 PHE   0.010   0.001   PHE R 290 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 2270)
  covalent geometry    : angle       0.49387 ( 3109)
  SS BOND              : bond        0.00141 (    1)
  SS BOND              : angle       0.97434 (    2)
  hydrogen bonds       : bond        0.06551 (  173)
  hydrogen bonds       : angle       4.15175 (  519)

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

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

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.136 
Fit side-chains
REVERT: R   36 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6925 (mtt)
  outliers start: 3
  outliers final: 2
  residues processed: 23
  average time/residue: 0.1071
  time to fit residues: 2.8255
Evaluate side-chains
  24 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.115460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.093663 restraints weight = 2791.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.2928 rms_B_bonded: 1.55
r_work: 0.2817 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2694 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2695
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2695 r_free = 0.2695    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2695 r_free = 0.2695    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2695
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.1378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2271  Z= 0.141
  Angle     :  0.485   7.777   3111  Z= 0.264
  Chirality :  0.039   0.126    378
  Planarity :  0.003   0.027    374
  Dihedral  :  4.333  22.742    319
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 12.56 %
    Favored  : 85.20 %
  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 (0.50), residues: 283
  helix:  2.22 (0.34), residues: 230
  sheet:  None (None), residues: 0
  loop : -0.66 (0.82), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 131 
 TYR   0.006   0.001   TYR R 199 
 PHE   0.009   0.001   PHE R 290 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 2270)
  covalent geometry    : angle       0.48497 ( 3109)
  SS BOND              : bond        0.00145 (    1)
  SS BOND              : angle       0.96428 (    2)
  hydrogen bonds       : bond        0.06417 (  173)
  hydrogen bonds       : angle       4.10039 (  519)

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

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

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 254 (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: 0.0959
  time to fit residues: 2.7294
Evaluate side-chains
  24 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 0 optimal weight:    9.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.114441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.092748 restraints weight = 2855.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.2914 rms_B_bonded: 1.56
r_work: 0.2802 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2680 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2673
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2673 r_free = 0.2673    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2673 r_free = 0.2673    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2673
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.1390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2271  Z= 0.150
  Angle     :  0.491   7.876   3111  Z= 0.269
  Chirality :  0.039   0.128    378
  Planarity :  0.003   0.027    374
  Dihedral  :  4.383  22.848    319
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 2.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 11.66 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.48 (0.50), residues: 283
  helix:  2.17 (0.34), residues: 230
  sheet:  None (None), residues: 0
  loop : -0.74 (0.81), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 151 
 TYR   0.007   0.001   TYR R 199 
 PHE   0.010   0.001   PHE R 290 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 2270)
  covalent geometry    : angle       0.49052 ( 3109)
  SS BOND              : bond        0.00171 (    1)
  SS BOND              : angle       0.96699 (    2)
  hydrogen bonds       : bond        0.06722 (  173)
  hydrogen bonds       : angle       4.13109 (  519)

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

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

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.077 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 23
  average time/residue: 0.0993
  time to fit residues: 2.6015
Evaluate side-chains
  24 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0170
   chunk 12 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 20 optimal weight:    0.1980
   chunk 9 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.116575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.094909 restraints weight = 2826.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 1.55
r_work: 0.2834 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2711 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2707
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2707 r_free = 0.2707    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2707 r_free = 0.2707    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2707
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.1408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2271  Z= 0.131
  Angle     :  0.468   7.437   3111  Z= 0.255
  Chirality :  0.038   0.124    378
  Planarity :  0.003   0.026    374
  Dihedral  :  4.272  22.749    319
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.00 %
    Favored  : 85.20 %
  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 (0.50), residues: 283
  helix:  2.26 (0.34), residues: 230
  sheet:  None (None), residues: 0
  loop : -0.77 (0.81), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 131 
 TYR   0.006   0.001   TYR R 199 
 PHE   0.009   0.001   PHE R 290 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 2270)
  covalent geometry    : angle       0.46793 ( 3109)
  SS BOND              : bond        0.00169 (    1)
  SS BOND              : angle       0.96767 (    2)
  hydrogen bonds       : bond        0.06085 (  173)
  hydrogen bonds       : angle       4.03036 (  519)

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

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

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 20
  time to evaluate  : 0.048 
Fit side-chains
REVERT: R   36 MET cc_start: 0.7045 (mtt) cc_final: 0.6819 (mtt)
  outliers start: 4
  outliers final: 4
  residues processed: 23
  average time/residue: 0.1015
  time to fit residues: 2.6255
Evaluate side-chains
  24 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 20
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 27 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.114506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.092700 restraints weight = 2916.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.2917 rms_B_bonded: 1.59
r_work: 0.2803 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2680 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2674
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2674 r_free = 0.2674    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2674 r_free = 0.2674    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2674
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.1429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2271  Z= 0.150
  Angle     :  0.486   7.603   3111  Z= 0.267
  Chirality :  0.039   0.126    378
  Planarity :  0.003   0.027    374
  Dihedral  :  4.363  22.806    319
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.45 %
    Favored  : 84.75 %
  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:  2.48 (0.50), residues: 283
  helix:  2.18 (0.34), residues: 230
  sheet:  None (None), residues: 0
  loop : -0.81 (0.80), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 151 
 TYR   0.007   0.001   TYR R 199 
 PHE   0.010   0.001   PHE R 290 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 2270)
  covalent geometry    : angle       0.48579 ( 3109)
  SS BOND              : bond        0.00180 (    1)
  SS BOND              : angle       0.95973 (    2)
  hydrogen bonds       : bond        0.06688 (  173)
  hydrogen bonds       : angle       4.09768 (  519)

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

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

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.086 
Fit side-chains
REVERT: R   36 MET cc_start: 0.7136 (mtt) cc_final: 0.6903 (mtt)
  outliers start: 4
  outliers final: 4
  residues processed: 24
  average time/residue: 0.1019
  time to fit residues: 2.7979
Evaluate side-chains
  25 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 10 optimal weight:    0.2980
   chunk 16 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.114971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.093144 restraints weight = 2906.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.2931 rms_B_bonded: 1.59
r_work: 0.2815 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2691 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2676
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2677 r_free = 0.2677    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2677
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2271  Z= 0.142
  Angle     :  0.479   7.460   3111  Z= 0.262
  Chirality :  0.039   0.126    378
  Planarity :  0.003   0.027    374
  Dihedral  :  4.335  22.831    319
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.00 %
    Favored  : 84.75 %
  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:  2.50 (0.50), residues: 283
  helix:  2.21 (0.34), residues: 230
  sheet:  None (None), residues: 0
  loop : -0.85 (0.78), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 151 
 TYR   0.007   0.001   TYR R 199 
 PHE   0.009   0.001   PHE R 290 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 2270)
  covalent geometry    : angle       0.47818 ( 3109)
  SS BOND              : bond        0.00162 (    1)
  SS BOND              : angle       0.96669 (    2)
  hydrogen bonds       : bond        0.06497 (  173)
  hydrogen bonds       : angle       4.07310 (  519)

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

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

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.087 
Fit side-chains
REVERT: R   36 MET cc_start: 0.7179 (mtt) cc_final: 0.6913 (mtt)
  outliers start: 5
  outliers final: 4
  residues processed: 25
  average time/residue: 0.0761
  time to fit residues: 2.2151
Evaluate side-chains
  25 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0980
   chunk 9 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.116130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.094226 restraints weight = 2894.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.2940 rms_B_bonded: 1.59
r_work: 0.2828 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2704 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2705
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2705
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2271  Z= 0.133
  Angle     :  0.469   7.312   3111  Z= 0.256
  Chirality :  0.039   0.124    378
  Planarity :  0.003   0.027    374
  Dihedral  :  4.282  22.760    319
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.45 %
    Favored  : 84.75 %
  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 (0.50), residues: 283
  helix:  2.26 (0.34), residues: 230
  sheet:  None (None), residues: 0
  loop : -0.84 (0.78), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 151 
 TYR   0.006   0.001   TYR R 199 
 PHE   0.009   0.001   PHE R 290 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 2270)
  covalent geometry    : angle       0.46884 ( 3109)
  SS BOND              : bond        0.00162 (    1)
  SS BOND              : angle       0.96751 (    2)
  hydrogen bonds       : bond        0.06138 (  173)
  hydrogen bonds       : angle       4.02697 (  519)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 917.43 seconds
wall clock time: 17 minutes 4.23 seconds (1024.23 seconds total)