Starting phenix.real_space_refine
on Fri Aug 22 16:18:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rb7_19027/08_2025/8rb7_19027.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rb7_19027/08_2025/8rb7_19027.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rb7_19027/08_2025/8rb7_19027.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rb7_19027/08_2025/8rb7_19027.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rb7_19027/08_2025/8rb7_19027.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rb7_19027/08_2025/8rb7_19027.cif"
  }
  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=   0.001 sd=   0.007
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: 5
    Type Number    sf(0)   Gaussians
     S      14      5.16       5
     C    1840      2.51       5
     N     508      2.21       5
     O     538      1.98       5
     H    2948      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 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: 5848
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2924
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 2924
          Classifications: {'peptide': 180}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 169}
    Chain: "B"
      Number of atoms: 2924
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 2924
          Classifications: {'peptide': 180}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 169}
  Time building chain proxies: 1.54, per 1000 atoms: 0.26
  Number of scatterers: 5848
  At special positions: 0
  Unit cell: (73.216, 134.784, 50.752, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     O     538      8.00
     N     508      7.00
     C    1840      6.00
     H    2948      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.49
  Conformation dependent library (CDL) restraints added in 128.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  688

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 0 sheets defined
      73.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 180 through 194
    Processing helix  chain 'A' and resid 198 through 208
      removed outlier: 3.553A  pdb=" N   ARG A 204 " --> pdb=" O   ALA A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 211
      No H-bonds generated for 'chain 'A' and resid 209 through 211'
    Processing helix  chain 'A' and resid 212 through 225
    Processing helix  chain 'A' and resid 229 through 242
    Processing helix  chain 'A' and resid 246 through 256
    Processing helix  chain 'A' and resid 264 through 282
    Processing helix  chain 'A' and resid 286 through 288
      No H-bonds generated for 'chain 'A' and resid 286 through 288'
    Processing helix  chain 'A' and resid 289 through 302
    Processing helix  chain 'A' and resid 305 through 319
      removed outlier: 4.203A  pdb=" N   GLY A 319 " --> pdb=" O   LEU A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 336
    Processing helix  chain 'B' and resid 180 through 194
      removed outlier: 3.625A  pdb=" N   TRP B 184 " --> pdb=" O   PRO B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 208
    Processing helix  chain 'B' and resid 209 through 211
      No H-bonds generated for 'chain 'B' and resid 209 through 211'
    Processing helix  chain 'B' and resid 212 through 225
      removed outlier: 3.599A  pdb=" N   ASN B 225 " --> pdb=" O   VAL B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 242
    Processing helix  chain 'B' and resid 246 through 256
    Processing helix  chain 'B' and resid 264 through 282
      removed outlier: 3.808A  pdb=" N   LEU B 275 " --> pdb=" O   ARG B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 288
      No H-bonds generated for 'chain 'B' and resid 286 through 288'
    Processing helix  chain 'B' and resid 289 through 302
    Processing helix  chain 'B' and resid 305 through 319
    Processing helix  chain 'B' and resid 323 through 336

    177 hydrogen bonds defined for protein.
    531 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: 1.19

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        0.90 -     1.09: 818
        1.09 -     1.27: 2629
        1.27 -     1.45: 737
        1.45 -     1.63: 1696
        1.63 -     1.82: 22
  Bond restraints: 5902
  Sorted by residual:
  bond pdb=" N   THR A 189 "
       pdb=" H   THR A 189 "
    ideal  model  delta    sigma   weight residual
    0.860  1.012 -0.152 2.00e-02 2.50e+03 5.78e+01
  bond pdb=" N   LYS A 164 "
       pdb=" H   LYS A 164 "
    ideal  model  delta    sigma   weight residual
    0.860  1.012 -0.152 2.00e-02 2.50e+03 5.75e+01
  bond pdb=" NH1 ARG A 166 "
       pdb="HH12 ARG A 166 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.73e+01
  bond pdb=" NH1 ARG A 278 "
       pdb="HH12 ARG A 278 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.73e+01
  bond pdb=" CE1 PHE A 168 "
       pdb=" HE1 PHE A 168 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.73e+01
  ... (remaining 5897 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.47: 8860
        2.47 -     4.94: 1406
        4.94 -     7.40: 387
        7.40 -     9.87: 63
        9.87 -    12.34: 6
  Bond angle restraints: 10722
  Sorted by residual:
  angle pdb=" C   ASP A 317 "
        pdb=" N   GLN A 318 "
        pdb=" CA  GLN A 318 "
      ideal   model   delta    sigma   weight residual
     120.38  127.94   -7.56 1.37e+00 5.33e-01 3.05e+01
  angle pdb=" C   ASP B 317 "
        pdb=" N   GLN B 318 "
        pdb=" CA  GLN B 318 "
      ideal   model   delta    sigma   weight residual
     120.28  127.60   -7.32 1.34e+00 5.57e-01 2.98e+01
  angle pdb=" C   SER B 250 "
        pdb=" N   GLN B 251 "
        pdb=" CA  GLN B 251 "
      ideal   model   delta    sigma   weight residual
     120.44  127.48   -7.04 1.30e+00 5.92e-01 2.93e+01
  angle pdb=" C   SER A 250 "
        pdb=" N   GLN A 251 "
        pdb=" CA  GLN A 251 "
      ideal   model   delta    sigma   weight residual
     120.44  127.35   -6.91 1.30e+00 5.92e-01 2.83e+01
  angle pdb=" C   LYS B 238 "
        pdb=" N   GLN B 239 "
        pdb=" CA  GLN B 239 "
      ideal   model   delta    sigma   weight residual
     120.28  127.12   -6.84 1.34e+00 5.57e-01 2.61e+01
  ... (remaining 10717 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.31: 2475
       18.31 -    36.62: 155
       36.62 -    54.94: 59
       54.94 -    73.25: 40
       73.25 -    91.56: 7
  Dihedral angle restraints: 2736
    sinusoidal: 1546
      harmonic: 1190
  Sorted by residual:
  dihedral pdb=" CA  PRO B 322 "
           pdb=" C   PRO B 322 "
           pdb=" N   THR B 323 "
           pdb=" CA  THR B 323 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.26   28.74     0      5.00e+00 4.00e-02 3.30e+01
  dihedral pdb=" CA  PRO A 322 "
           pdb=" C   PRO A 322 "
           pdb=" N   THR A 323 "
           pdb=" CA  THR A 323 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.96   27.04     0      5.00e+00 4.00e-02 2.92e+01
  dihedral pdb=" CA  GLU B 179 "
           pdb=" C   GLU B 179 "
           pdb=" N   PRO B 180 "
           pdb=" CA  PRO B 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.41   24.59     0      5.00e+00 4.00e-02 2.42e+01
  ... (remaining 2733 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 282
       0.083 -    0.165: 128
       0.165 -    0.247: 20
       0.247 -    0.329: 6
       0.329 -    0.411: 6
  Chirality restraints: 442
  Sorted by residual:
  chirality pdb=" CA  GLN B 313 "
            pdb=" N   GLN B 313 "
            pdb=" C   GLN B 313 "
            pdb=" CB  GLN B 313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.23e+00
  chirality pdb=" CA  GLN A 251 "
            pdb=" N   GLN A 251 "
            pdb=" C   GLN A 251 "
            pdb=" CB  GLN A 251 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.26e+00
  chirality pdb=" CA  LYS B 161 "
            pdb=" N   LYS B 161 "
            pdb=" C   LYS B 161 "
            pdb=" CB  LYS B 161 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.23e+00
  ... (remaining 439 not shown)

  Planarity restraints: 856
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 251 "    0.080 2.00e-02 2.50e+03   4.80e-01 3.46e+03
        pdb=" CD  GLN A 251 "    0.011 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 251 "   -0.085 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 251 "    0.000 2.00e-02 2.50e+03
        pdb="HE21 GLN A 251 "    0.824 2.00e-02 2.50e+03
        pdb="HE22 GLN A 251 "   -0.830 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 313 "    0.301 2.00e-02 2.50e+03   4.16e-01 2.59e+03
        pdb=" CD  GLN B 313 "   -0.007 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 313 "   -0.290 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 313 "   -0.002 2.00e-02 2.50e+03
        pdb="HE21 GLN B 313 "    0.655 2.00e-02 2.50e+03
        pdb="HE22 GLN B 313 "   -0.658 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 318 "   -0.312 2.00e-02 2.50e+03   3.99e-01 2.38e+03
        pdb=" CD  GLN A 318 "    0.021 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 318 "    0.306 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 318 "    0.005 2.00e-02 2.50e+03
        pdb="HE21 GLN A 318 "   -0.627 2.00e-02 2.50e+03
        pdb="HE22 GLN A 318 "    0.607 2.00e-02 2.50e+03
  ... (remaining 853 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 304
        2.18 -     2.78: 10349
        2.78 -     3.39: 16154
        3.39 -     3.99: 19956
        3.99 -     4.60: 29203
  Nonbonded interactions: 75966
  Sorted by model distance:
  nonbonded pdb="HH11 ARG A 247 "
            pdb=" OE1 GLN B 292 "
     model   vdw
     1.570 2.450
  nonbonded pdb=" HG  SER A 266 "
            pdb=" OE1 GLU A 335 "
     model   vdw
     1.595 2.450
  nonbonded pdb=" OE1 GLU B 245 "
            pdb=" HG1 THR B 249 "
     model   vdw
     1.634 2.450
  nonbonded pdb=" HG  SER B 229 "
            pdb=" OE1 GLU B 232 "
     model   vdw
     1.637 2.450
  nonbonded pdb=" O   VAL B 206 "
            pdb=" HG  SER B 209 "
     model   vdw
     1.653 2.450
  ... (remaining 75961 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.030
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.710
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
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      :  0.014   0.117   2954  Z= 0.813
  Angle     :  1.834   8.004   3992  Z= 1.226
  Chirality :  0.099   0.411    442
  Planarity :  0.016   0.103    518
  Dihedral  : 14.959  91.559   1150
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 0.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  2.88 %
    Favored  : 96.15 %
  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: -1.02 (0.40), residues: 356
  helix: -0.79 (0.28), residues: 243
  sheet:  None (None), residues: 0
  loop :  0.03 (0.61), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 248 
 TYR   0.142   0.017   TYR B 162 
 PHE   0.045   0.014   PHE A 237 
 TRP   0.103   0.025   TRP A 205 
 HIS   0.011   0.005   HIS B 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.01421 ( 2954)
  covalent geometry    : angle       1.83429 ( 3992)
  hydrogen bonds       : bond        0.17452 (  177)
  hydrogen bonds       : angle       7.74227 (  531)

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 155
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 ARG cc_start: 0.7964 (ttp80) cc_final: 0.7437 (ttm170)
REVERT: A  306 ASN cc_start: 0.6725 (m-40) cc_final: 0.6311 (p0)
REVERT: B  291 ASP cc_start: 0.7782 (p0) cc_final: 0.7415 (p0)
  outliers start: 3
  outliers final: 1
  residues processed: 156
  average time/residue: 0.2871
  time to fit residues: 49.0057
Evaluate side-chains
  104 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  160 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 222 GLN
A 239 GLN
A 251 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.180577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.149960 restraints weight = 13420.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3847 rms_B_bonded: 4.23
r_work: 0.3690 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.4960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   2954  Z= 0.174
  Angle     :  0.658   5.226   3992  Z= 0.356
  Chirality :  0.038   0.156    442
  Planarity :  0.006   0.043    518
  Dihedral  :  5.742  22.889    395
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 11.22 %
    Favored  : 86.86 %
  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:  0.58 (0.43), residues: 356
  helix:  0.63 (0.31), residues: 248
  sheet:  None (None), residues: 0
  loop :  0.11 (0.62), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 287 
 TYR   0.015   0.002   TYR B 162 
 PHE   0.014   0.002   PHE A 181 
 TRP   0.015   0.002   TRP B 184 
 HIS   0.003   0.001   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 2954)
  covalent geometry    : angle       0.65758 ( 3992)
  hydrogen bonds       : bond        0.05595 (  177)
  hydrogen bonds       : angle       5.52225 (  531)

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 LYS cc_start: 0.6765 (tttt) cc_final: 0.6389 (pptt)
REVERT: A  218 MET cc_start: 0.9267 (tpp) cc_final: 0.8921 (tpt)
REVERT: A  256 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7386 (ttm170)
REVERT: A  292 GLN cc_start: 0.8799 (mt0) cc_final: 0.8571 (tp40)
REVERT: B  197 ILE cc_start: 0.8009 (mm) cc_final: 0.7636 (tp)
REVERT: B  211 ARG cc_start: 0.7892 (ptt90) cc_final: 0.6167 (mmt-90)
REVERT: B  263 GLU cc_start: 0.7295 (tt0) cc_final: 0.6987 (tt0)
REVERT: B  268 TYR cc_start: 0.8034 (t80) cc_final: 0.7598 (t80)
REVERT: B  291 ASP cc_start: 0.8212 (p0) cc_final: 0.7782 (p0)
REVERT: B  313 GLN cc_start: 0.8346 (tt0) cc_final: 0.7883 (tp-100)
  outliers start: 6
  outliers final: 3
  residues processed: 110
  average time/residue: 0.2239
  time to fit residues: 27.7149
Evaluate side-chains
  97 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 94
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  257 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 15 optimal weight:    9.9990
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    0.4980
   chunk 21 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 16 optimal weight:    9.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    2.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.181096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.150171 restraints weight = 13330.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3844 rms_B_bonded: 4.21
r_work: 0.3685 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.5865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2954  Z= 0.157
  Angle     :  0.588   5.302   3992  Z= 0.313
  Chirality :  0.037   0.156    442
  Planarity :  0.006   0.045    518
  Dihedral  :  5.059  19.377    394
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 12.82 %
    Favored  : 85.26 %
  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:  1.20 (0.44), residues: 356
  helix:  1.09 (0.32), residues: 248
  sheet:  None (None), residues: 0
  loop :  0.35 (0.63), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 166 
 TYR   0.013   0.002   TYR B 162 
 PHE   0.015   0.002   PHE A 181 
 TRP   0.011   0.002   TRP B 184 
 HIS   0.002   0.001   HIS B 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 2954)
  covalent geometry    : angle       0.58807 ( 3992)
  hydrogen bonds       : bond        0.04616 (  177)
  hydrogen bonds       : angle       5.14747 (  531)

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 LYS cc_start: 0.7299 (tttt) cc_final: 0.6614 (pptt)
REVERT: A  162 TYR cc_start: 0.7029 (m-80) cc_final: 0.5818 (m-80)
REVERT: A  177 GLU cc_start: 0.8808 (pt0) cc_final: 0.8325 (pm20)
REVERT: A  218 MET cc_start: 0.9182 (tpp) cc_final: 0.8756 (tpt)
REVERT: A  256 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7257 (ttm170)
REVERT: A  263 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7314 (mt-10)
REVERT: B  197 ILE cc_start: 0.8159 (mm) cc_final: 0.7619 (tp)
REVERT: B  211 ARG cc_start: 0.7930 (ptt90) cc_final: 0.6472 (mmt180)
REVERT: B  259 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7644 (tt0)
REVERT: B  268 TYR cc_start: 0.7954 (t80) cc_final: 0.7472 (t80)
REVERT: B  291 ASP cc_start: 0.7993 (p0) cc_final: 0.7522 (p0)
  outliers start: 6
  outliers final: 4
  residues processed: 110
  average time/residue: 0.2102
  time to fit residues: 26.1535
Evaluate side-chains
  95 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 SER
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  257 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 13 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 222 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.185986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.155358 restraints weight = 13281.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3854 rms_B_bonded: 4.16
r_work: 0.3693 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.6350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2954  Z= 0.120
  Angle     :  0.534   5.167   3992  Z= 0.280
  Chirality :  0.035   0.150    442
  Planarity :  0.005   0.049    518
  Dihedral  :  4.736  18.310    394
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 13.78 %
    Favored  : 84.94 %
  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:  1.46 (0.45), residues: 356
  helix:  1.32 (0.32), residues: 248
  sheet:  None (None), residues: 0
  loop :  0.37 (0.65), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 311 
 TYR   0.008   0.001   TYR B 162 
 PHE   0.011   0.001   PHE A 181 
 TRP   0.010   0.001   TRP A 184 
 HIS   0.001   0.001   HIS B 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 2954)
  covalent geometry    : angle       0.53352 ( 3992)
  hydrogen bonds       : bond        0.04082 (  177)
  hydrogen bonds       : angle       4.88350 (  531)

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 LYS cc_start: 0.7360 (tttt) cc_final: 0.6600 (pptt)
REVERT: A  177 GLU cc_start: 0.8834 (pt0) cc_final: 0.8361 (pm20)
REVERT: A  218 MET cc_start: 0.9189 (tpp) cc_final: 0.8782 (tpt)
REVERT: A  256 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7260 (ttm170)
REVERT: A  263 GLU cc_start: 0.7803 (mt-10) cc_final: 0.6986 (mt-10)
REVERT: A  315 LEU cc_start: 0.8438 (mt) cc_final: 0.8237 (mt)
REVERT: B  197 ILE cc_start: 0.8114 (mm) cc_final: 0.7578 (tp)
REVERT: B  211 ARG cc_start: 0.8066 (ptt90) cc_final: 0.6376 (mmt180)
REVERT: B  268 TYR cc_start: 0.7930 (t80) cc_final: 0.7710 (t80)
  outliers start: 4
  outliers final: 3
  residues processed: 105
  average time/residue: 0.2177
  time to fit residues: 25.7728
Evaluate side-chains
  94 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 91
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  257 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 6 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 35 optimal weight:    7.9990
   chunk 18 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 222 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.182761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.151570 restraints weight = 13303.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3850 rms_B_bonded: 4.19
r_work: 0.3692 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.6651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2954  Z= 0.124
  Angle     :  0.533   4.968   3992  Z= 0.278
  Chirality :  0.035   0.145    442
  Planarity :  0.005   0.036    518
  Dihedral  :  4.525  18.172    394
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 14.10 %
    Favored  : 84.62 %
  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:  1.55 (0.44), residues: 356
  helix:  1.39 (0.32), residues: 248
  sheet:  None (None), residues: 0
  loop :  0.36 (0.64), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 287 
 TYR   0.009   0.001   TYR B 162 
 PHE   0.012   0.001   PHE A 181 
 TRP   0.009   0.001   TRP A 184 
 HIS   0.001   0.001   HIS B 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 2954)
  covalent geometry    : angle       0.53275 ( 3992)
  hydrogen bonds       : bond        0.03901 (  177)
  hydrogen bonds       : angle       4.79588 (  531)

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 LYS cc_start: 0.7572 (tttt) cc_final: 0.6747 (pptt)
REVERT: A  162 TYR cc_start: 0.7277 (m-80) cc_final: 0.6098 (m-80)
REVERT: A  190 GLU cc_start: 0.8646 (tt0) cc_final: 0.8335 (tt0)
REVERT: A  218 MET cc_start: 0.9167 (tpp) cc_final: 0.8739 (tpt)
REVERT: A  256 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7231 (ttm170)
REVERT: A  264 LYS cc_start: 0.8466 (mtmt) cc_final: 0.8091 (ttpt)
REVERT: B  197 ILE cc_start: 0.8099 (mm) cc_final: 0.7863 (tp)
REVERT: B  211 ARG cc_start: 0.8196 (ptt90) cc_final: 0.6404 (mmt180)
  outliers start: 4
  outliers final: 2
  residues processed: 102
  average time/residue: 0.1960
  time to fit residues: 22.8175
Evaluate side-chains
  97 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain B residue  257 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 35 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 15 optimal weight:   10.0000
   chunk 4 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 10 optimal weight:    5.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 222 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.179809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.147745 restraints weight = 13290.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3820 rms_B_bonded: 4.27
r_work: 0.3662 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.7000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2954  Z= 0.152
  Angle     :  0.535   4.915   3992  Z= 0.284
  Chirality :  0.036   0.148    442
  Planarity :  0.005   0.029    518
  Dihedral  :  4.435  18.428    394
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.82 %
    Favored  : 85.58 %
  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:  1.45 (0.44), residues: 356
  helix:  1.34 (0.32), residues: 248
  sheet:  None (None), residues: 0
  loop :  0.27 (0.63), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 287 
 TYR   0.010   0.002   TYR B 162 
 PHE   0.010   0.001   PHE B 181 
 TRP   0.008   0.001   TRP B 184 
 HIS   0.001   0.001   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 2954)
  covalent geometry    : angle       0.53502 ( 3992)
  hydrogen bonds       : bond        0.04069 (  177)
  hydrogen bonds       : angle       4.87505 (  531)

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 LYS cc_start: 0.7546 (tttt) cc_final: 0.6703 (pptt)
REVERT: A  162 TYR cc_start: 0.7465 (m-80) cc_final: 0.6176 (m-80)
REVERT: A  218 MET cc_start: 0.9172 (tpp) cc_final: 0.8704 (tpt)
REVERT: A  256 ARG cc_start: 0.7993 (ttp80) cc_final: 0.7182 (ttm170)
REVERT: A  264 LYS cc_start: 0.8523 (mtmt) cc_final: 0.8125 (ttpt)
REVERT: B  162 TYR cc_start: 0.7339 (t80) cc_final: 0.4784 (t80)
REVERT: B  197 ILE cc_start: 0.8047 (mm) cc_final: 0.7808 (tp)
REVERT: B  211 ARG cc_start: 0.8261 (ptt90) cc_final: 0.6546 (mmt180)
  outliers start: 5
  outliers final: 3
  residues processed: 99
  average time/residue: 0.2180
  time to fit residues: 24.4231
Evaluate side-chains
  95 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 92
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 SER
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  257 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 16 optimal weight:    0.0170
   chunk 34 optimal weight:    8.9990
   chunk 4 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 12 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.8024

-------------------------------------------------------------------------------
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 = 0.4247 r_free = 0.4247 target = 0.183653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.152077 restraints weight = 13252.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3835 rms_B_bonded: 4.23
r_work: 0.3676 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.7144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2954  Z= 0.125
  Angle     :  0.520   4.925   3992  Z= 0.274
  Chirality :  0.035   0.149    442
  Planarity :  0.005   0.030    518
  Dihedral  :  4.272  17.983    394
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 14.10 %
    Favored  : 85.26 %
  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:  1.59 (0.45), residues: 356
  helix:  1.48 (0.32), residues: 248
  sheet:  None (None), residues: 0
  loop :  0.23 (0.63), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 287 
 TYR   0.008   0.001   TYR B 162 
 PHE   0.013   0.001   PHE A 181 
 TRP   0.009   0.001   TRP A 184 
 HIS   0.001   0.001   HIS B 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 2954)
  covalent geometry    : angle       0.52029 ( 3992)
  hydrogen bonds       : bond        0.03771 (  177)
  hydrogen bonds       : angle       4.70723 (  531)

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 LYS cc_start: 0.7681 (tttt) cc_final: 0.6697 (pptt)
REVERT: A  162 TYR cc_start: 0.7437 (m-80) cc_final: 0.6160 (m-80)
REVERT: A  218 MET cc_start: 0.9171 (tpp) cc_final: 0.8687 (tpt)
REVERT: A  256 ARG cc_start: 0.7979 (ttp80) cc_final: 0.7154 (ttm170)
REVERT: A  264 LYS cc_start: 0.8470 (mtmt) cc_final: 0.8082 (ttpt)
REVERT: B  162 TYR cc_start: 0.7435 (t80) cc_final: 0.4386 (p90)
REVERT: B  197 ILE cc_start: 0.8068 (mm) cc_final: 0.7499 (tp)
REVERT: B  211 ARG cc_start: 0.8260 (ptt90) cc_final: 0.6529 (mmt180)
  outliers start: 2
  outliers final: 1
  residues processed: 101
  average time/residue: 0.2275
  time to fit residues: 25.8609
Evaluate side-chains
  89 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 31 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 16 optimal weight:    9.9990
   chunk 14 optimal weight:    0.8980
   chunk 25 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.4261 r_free = 0.4261 target = 0.185134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.153655 restraints weight = 13095.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3853 rms_B_bonded: 4.22
r_work: 0.3692 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.7319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2954  Z= 0.111
  Angle     :  0.513   4.814   3992  Z= 0.267
  Chirality :  0.035   0.143    442
  Planarity :  0.005   0.058    518
  Dihedral  :  4.101  17.452    394
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 15.71 %
    Favored  : 83.65 %
  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:  1.71 (0.45), residues: 356
  helix:  1.59 (0.33), residues: 248
  sheet:  None (None), residues: 0
  loop :  0.21 (0.64), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 287 
 TYR   0.006   0.001   TYR B 162 
 PHE   0.008   0.001   PHE A 181 
 TRP   0.009   0.001   TRP A 184 
 HIS   0.001   0.000   HIS B 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 2954)
  covalent geometry    : angle       0.51258 ( 3992)
  hydrogen bonds       : bond        0.03535 (  177)
  hydrogen bonds       : angle       4.58555 (  531)

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 LYS cc_start: 0.7764 (tttt) cc_final: 0.6768 (pptt)
REVERT: A  162 TYR cc_start: 0.7404 (m-80) cc_final: 0.6150 (m-80)
REVERT: A  218 MET cc_start: 0.9156 (tpp) cc_final: 0.8696 (tpt)
REVERT: A  256 ARG cc_start: 0.7968 (ttp80) cc_final: 0.7136 (ttm170)
REVERT: A  264 LYS cc_start: 0.8409 (mtmt) cc_final: 0.8061 (ttpt)
REVERT: B  162 TYR cc_start: 0.7448 (t80) cc_final: 0.4341 (p90)
REVERT: B  197 ILE cc_start: 0.8043 (mm) cc_final: 0.7769 (tp)
  outliers start: 2
  outliers final: 1
  residues processed: 101
  average time/residue: 0.1944
  time to fit residues: 22.4516
Evaluate side-chains
  91 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 90
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0970
   chunk 11 optimal weight:    5.9990
   chunk 3 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    1.9984

-------------------------------------------------------------------------------
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 = 0.4241 r_free = 0.4241 target = 0.183353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.151165 restraints weight = 13221.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3828 rms_B_bonded: 4.28
r_work: 0.3668 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.7403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2954  Z= 0.130
  Angle     :  0.515   4.843   3992  Z= 0.271
  Chirality :  0.035   0.144    442
  Planarity :  0.005   0.045    518
  Dihedral  :  4.077  17.679    394
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 15.71 %
    Favored  : 83.65 %
  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:  1.74 (0.45), residues: 356
  helix:  1.62 (0.33), residues: 249
  sheet:  None (None), residues: 0
  loop :  0.19 (0.62), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 287 
 TYR   0.009   0.001   TYR B 162 
 PHE   0.016   0.001   PHE A 181 
 TRP   0.008   0.001   TRP A 184 
 HIS   0.001   0.001   HIS B 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 2954)
  covalent geometry    : angle       0.51462 ( 3992)
  hydrogen bonds       : bond        0.03733 (  177)
  hydrogen bonds       : angle       4.61054 (  531)

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 90
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 LYS cc_start: 0.7832 (tttt) cc_final: 0.6825 (pptt)
REVERT: A  162 TYR cc_start: 0.7467 (m-80) cc_final: 0.6144 (m-80)
REVERT: A  235 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8662 (mm-30)
REVERT: A  256 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7131 (ttm170)
REVERT: A  263 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7503 (tt0)
REVERT: A  264 LYS cc_start: 0.8507 (mtmt) cc_final: 0.8012 (ttpt)
REVERT: B  162 TYR cc_start: 0.7626 (t80) cc_final: 0.4533 (p90)
REVERT: B  197 ILE cc_start: 0.8132 (mm) cc_final: 0.7574 (tp)
REVERT: B  283 ARG cc_start: 0.7449 (ttm110) cc_final: 0.6756 (tpp80)
REVERT: B  292 GLN cc_start: 0.8921 (mt0) cc_final: 0.8467 (tp40)
  outliers start: 2
  outliers final: 1
  residues processed: 92
  average time/residue: 0.1889
  time to fit residues: 19.9970
Evaluate side-chains
  91 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 90
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 34 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 7 optimal weight:    0.2980
   chunk 16 optimal weight:    0.4980
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.4258 r_free = 0.4258 target = 0.185108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.152735 restraints weight = 13307.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3855 rms_B_bonded: 4.34
r_work: 0.3695 rms_B_bonded: 4.89 restraints_weight: 0.5000
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.7502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   2954  Z= 0.108
  Angle     :  0.506   4.796   3992  Z= 0.262
  Chirality :  0.035   0.144    442
  Planarity :  0.005   0.047    518
  Dihedral  :  3.980  17.091    394
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 16.67 %
    Favored  : 83.01 %
  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:  1.88 (0.45), residues: 356
  helix:  1.70 (0.33), residues: 249
  sheet:  None (None), residues: 0
  loop :  0.34 (0.63), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 287 
 TYR   0.006   0.001   TYR B 162 
 PHE   0.008   0.001   PHE A 181 
 TRP   0.008   0.001   TRP A 184 
 HIS   0.001   0.001   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 2954)
  covalent geometry    : angle       0.50592 ( 3992)
  hydrogen bonds       : bond        0.03479 (  177)
  hydrogen bonds       : angle       4.46536 (  531)

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 LYS cc_start: 0.7828 (tttt) cc_final: 0.6802 (pptt)
REVERT: A  162 TYR cc_start: 0.7420 (m-80) cc_final: 0.6087 (m-80)
REVERT: A  208 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8570 (tm-30)
REVERT: A  218 MET cc_start: 0.9069 (tpp) cc_final: 0.8813 (tpt)
REVERT: A  235 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8661 (mm-30)
REVERT: A  256 ARG cc_start: 0.8003 (ttp80) cc_final: 0.7138 (ttm170)
REVERT: A  263 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7498 (tt0)
REVERT: A  264 LYS cc_start: 0.8339 (mtmt) cc_final: 0.7859 (ttpt)
REVERT: B  162 TYR cc_start: 0.7505 (t80) cc_final: 0.4510 (p90)
REVERT: B  197 ILE cc_start: 0.8121 (mm) cc_final: 0.7564 (tp)
REVERT: B  283 ARG cc_start: 0.7480 (ttm110) cc_final: 0.6851 (tpp80)
REVERT: B  292 GLN cc_start: 0.8892 (mt0) cc_final: 0.8438 (tp40)
  outliers start: 1
  outliers final: 1
  residues processed: 94
  average time/residue: 0.2131
  time to fit residues: 22.8189
Evaluate side-chains
  92 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 35 optimal weight:    6.9990
   chunk 10 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.4250 r_free = 0.4250 target = 0.184462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.153306 restraints weight = 12888.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3871 rms_B_bonded: 4.08
r_work: 0.3715 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.7633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   2954  Z= 0.105
  Angle     :  0.504   4.808   3992  Z= 0.260
  Chirality :  0.034   0.144    442
  Planarity :  0.005   0.044    518
  Dihedral  :  3.858  16.856    394
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 16.67 %
    Favored  : 83.33 %
  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:  2.01 (0.45), residues: 356
  helix:  1.81 (0.33), residues: 250
  sheet:  None (None), residues: 0
  loop :  0.33 (0.64), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 287 
 TYR   0.006   0.001   TYR B 162 
 PHE   0.008   0.001   PHE A 181 
 TRP   0.010   0.001   TRP A 184 
 HIS   0.001   0.001   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 2954)
  covalent geometry    : angle       0.50371 ( 3992)
  hydrogen bonds       : bond        0.03370 (  177)
  hydrogen bonds       : angle       4.40663 (  531)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1971.46 seconds
wall clock time: 34 minutes 10.41 seconds (2050.41 seconds total)