Starting phenix.real_space_refine
on Fri Aug 22 19:18:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6coy_7544/08_2025/6coy_7544.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6coy_7544/08_2025/6coy_7544.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6coy_7544/08_2025/6coy_7544.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6coy_7544/08_2025/6coy_7544.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6coy_7544/08_2025/6coy_7544.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6coy_7544/08_2025/6coy_7544.cif"
  }
  resolution = 3.36
  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=   0.003
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      58      5.16       5
     Cl      4      4.86       5
     C    4776      2.51       5
     N    1130      2.21       5
     O    1188      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  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: 7156
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 465, 3576
          Classifications: {'peptide': 465}
          Link IDs: {'PTRANS': 25, 'TRANS': 439}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CL': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.32, per 1000 atoms: 0.32
  Number of scatterers: 7156
  At special positions: 0
  Unit cell: (110.21, 77.25, 76.22, 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)
     Cl      4     17.00
     S      58     16.00
     O    1188      8.00
     N    1130      7.00
     C    4776      6.00
    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: 0.57
  Conformation dependent library (CDL) restraints added in 277.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1708

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 3 sheets defined
      78.8% alpha, 1.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 116 through 152
    Processing helix  chain 'A' and resid 156 through 183
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 184 through 187
    Processing helix  chain 'A' and resid 190 through 199
    Processing helix  chain 'A' and resid 203 through 207
    Processing helix  chain 'A' and resid 208 through 224
    Processing helix  chain 'A' and resid 231 through 250
    Processing helix  chain 'A' and resid 263 through 280
      removed outlier: 3.538A  pdb=" N   THR A 268 " --> pdb=" O   SER A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 292
    Processing helix  chain 'A' and resid 299 through 323
    Processing helix  chain 'A' and resid 344 through 346
      No H-bonds generated for 'chain 'A' and resid 344 through 346'
    Processing helix  chain 'A' and resid 347 through 379
    Processing helix  chain 'A' and resid 381 through 389
      removed outlier: 3.707A  pdb=" N   LYS A 388 " --> pdb=" O   GLN A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 406
    Processing helix  chain 'A' and resid 410 through 414
    Processing helix  chain 'A' and resid 419 through 428
    Processing helix  chain 'A' and resid 432 through 436
    Processing helix  chain 'A' and resid 439 through 450
      removed outlier: 6.892A  pdb=" N   GLN A 445 " --> pdb=" O   SER A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 475
    Processing helix  chain 'A' and resid 483 through 503
    Processing helix  chain 'A' and resid 521 through 538
    Processing helix  chain 'A' and resid 541 through 551
    Processing helix  chain 'A' and resid 555 through 571
    Processing helix  chain 'A' and resid 576 through 585
    Processing helix  chain 'B' and resid 117 through 152
    Processing helix  chain 'B' and resid 156 through 183
      Proline residue:  B 168  - end of helix
    Processing helix  chain 'B' and resid 184 through 187
    Processing helix  chain 'B' and resid 190 through 199
    Processing helix  chain 'B' and resid 203 through 207
    Processing helix  chain 'B' and resid 208 through 224
    Processing helix  chain 'B' and resid 231 through 250
    Processing helix  chain 'B' and resid 263 through 280
      removed outlier: 3.538A  pdb=" N   THR B 268 " --> pdb=" O   SER B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 292
    Processing helix  chain 'B' and resid 299 through 323
    Processing helix  chain 'B' and resid 344 through 346
      No H-bonds generated for 'chain 'B' and resid 344 through 346'
    Processing helix  chain 'B' and resid 347 through 379
    Processing helix  chain 'B' and resid 381 through 389
      removed outlier: 3.707A  pdb=" N   LYS B 388 " --> pdb=" O   GLN B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 406
    Processing helix  chain 'B' and resid 410 through 414
    Processing helix  chain 'B' and resid 419 through 428
    Processing helix  chain 'B' and resid 432 through 436
    Processing helix  chain 'B' and resid 439 through 450
      removed outlier: 6.892A  pdb=" N   GLN B 445 " --> pdb=" O   SER B 442 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 475
    Processing helix  chain 'B' and resid 483 through 503
    Processing helix  chain 'B' and resid 521 through 538
    Processing helix  chain 'B' and resid 541 through 551
    Processing helix  chain 'B' and resid 555 through 571
    Processing helix  chain 'B' and resid 576 through 585
    Processing sheet with id=AA1, first strand: chain 'A' and resid 296 through 298
    Processing sheet with id=AA2, first strand: chain 'A' and resid 510 through 512
    Processing sheet with id=AA3, first strand: chain 'B' and resid 510 through 512

    551 hydrogen bonds defined for protein.
    1551 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: 1.22

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1096
        1.31 -     1.43: 2014
        1.43 -     1.56: 4140
        1.56 -     1.68: 4
        1.68 -     1.81: 98
  Bond restraints: 7352
  Sorted by residual:
  bond pdb=" CB  ILE A 556 "
       pdb=" CG1 ILE A 556 "
    ideal  model  delta    sigma   weight residual
    1.530  1.377  0.153 2.00e-02 2.50e+03 5.83e+01
  bond pdb=" CB  ILE B 556 "
       pdb=" CG1 ILE B 556 "
    ideal  model  delta    sigma   weight residual
    1.530  1.377  0.153 2.00e-02 2.50e+03 5.83e+01
  bond pdb=" CB  HIS B 538 "
       pdb=" CG  HIS B 538 "
    ideal  model  delta    sigma   weight residual
    1.497  1.424  0.073 1.40e-02 5.10e+03 2.74e+01
  bond pdb=" CB  HIS A 538 "
       pdb=" CG  HIS A 538 "
    ideal  model  delta    sigma   weight residual
    1.497  1.424  0.073 1.40e-02 5.10e+03 2.74e+01
  bond pdb=" CB  ILE B 553 "
       pdb=" CG1 ILE B 553 "
    ideal  model  delta    sigma   weight residual
    1.530  1.431  0.099 2.00e-02 2.50e+03 2.44e+01
  ... (remaining 7347 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.64: 9310
        2.64 -     5.28: 636
        5.28 -     7.91: 52
        7.91 -    10.55: 6
       10.55 -    13.19: 2
  Bond angle restraints: 10006
  Sorted by residual:
  angle pdb=" C   THR B 281 "
        pdb=" N   PRO B 282 "
        pdb=" CA  PRO B 282 "
      ideal   model   delta    sigma   weight residual
     119.24  127.81   -8.57 1.04e+00 9.25e-01 6.80e+01
  angle pdb=" C   THR A 281 "
        pdb=" N   PRO A 282 "
        pdb=" CA  PRO A 282 "
      ideal   model   delta    sigma   weight residual
     119.24  127.81   -8.57 1.04e+00 9.25e-01 6.80e+01
  angle pdb=" C   LEU A 520 "
        pdb=" N   PRO A 521 "
        pdb=" CA  PRO A 521 "
      ideal   model   delta    sigma   weight residual
     119.47  128.00   -8.53 1.16e+00 7.43e-01 5.41e+01
  angle pdb=" C   LEU B 520 "
        pdb=" N   PRO B 521 "
        pdb=" CA  PRO B 521 "
      ideal   model   delta    sigma   weight residual
     119.47  128.00   -8.53 1.16e+00 7.43e-01 5.41e+01
  angle pdb=" C   PHE B 341 "
        pdb=" N   PRO B 342 "
        pdb=" CA  PRO B 342 "
      ideal   model   delta    sigma   weight residual
     119.56  125.93   -6.37 1.01e+00 9.80e-01 3.97e+01
  ... (remaining 10001 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.23: 4126
       17.23 -    34.46: 86
       34.46 -    51.69: 18
       51.69 -    68.91: 18
       68.91 -    86.14: 6
  Dihedral angle restraints: 4254
    sinusoidal: 1592
      harmonic: 2662
  Sorted by residual:
  dihedral pdb=" CA  THR B 432 "
           pdb=" C   THR B 432 "
           pdb=" N   TRP B 433 "
           pdb=" CA  TRP B 433 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.59  -16.41     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CA  THR A 432 "
           pdb=" C   THR A 432 "
           pdb=" N   TRP A 433 "
           pdb=" CA  TRP A 433 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.59  -16.41     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" C   TYR B 393 "
           pdb=" N   TYR B 393 "
           pdb=" CA  TYR B 393 "
           pdb=" CB  TYR B 393 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.59    7.99     0      2.50e+00 1.60e-01 1.02e+01
  ... (remaining 4251 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 684
       0.069 -    0.139: 342
       0.139 -    0.208: 102
       0.208 -    0.278: 34
       0.278 -    0.347: 8
  Chirality restraints: 1170
  Sorted by residual:
  chirality pdb=" CA  PRO A 407 "
            pdb=" N   PRO A 407 "
            pdb=" C   PRO A 407 "
            pdb=" CB  PRO A 407 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.37    0.35 2.00e-01 2.50e+01 3.01e+00
  chirality pdb=" CA  PRO B 407 "
            pdb=" N   PRO B 407 "
            pdb=" C   PRO B 407 "
            pdb=" CB  PRO B 407 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.37    0.35 2.00e-01 2.50e+01 3.01e+00
  chirality pdb=" CA  PRO B 558 "
            pdb=" N   PRO B 558 "
            pdb=" C   PRO B 558 "
            pdb=" CB  PRO B 558 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.40    0.32 2.00e-01 2.50e+01 2.56e+00
  ... (remaining 1167 not shown)

  Planarity restraints: 1224
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 590 "   -0.099 5.00e-02 4.00e+02   1.50e-01 3.59e+01
        pdb=" N   PRO B 591 "    0.259 5.00e-02 4.00e+02
        pdb=" CA  PRO B 591 "   -0.086 5.00e-02 4.00e+02
        pdb=" CD  PRO B 591 "   -0.074 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 590 "    0.099 5.00e-02 4.00e+02   1.50e-01 3.59e+01
        pdb=" N   PRO A 591 "   -0.259 5.00e-02 4.00e+02
        pdb=" CA  PRO A 591 "    0.086 5.00e-02 4.00e+02
        pdb=" CD  PRO A 591 "    0.074 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 485 "    0.067 5.00e-02 4.00e+02   1.03e-01 1.71e+01
        pdb=" N   PRO B 486 "   -0.179 5.00e-02 4.00e+02
        pdb=" CA  PRO B 486 "    0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO B 486 "    0.056 5.00e-02 4.00e+02
  ... (remaining 1221 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1662
        2.77 -     3.31: 7383
        3.31 -     3.84: 12334
        3.84 -     4.37: 14469
        4.37 -     4.90: 24411
  Nonbonded interactions: 60259
  Sorted by model distance:
  nonbonded pdb=" N   GLN A 185 "
            pdb=" OE1 GLN A 185 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" N   GLN B 185 "
            pdb=" OE1 GLN B 185 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" CB  GLU A 291 "
            pdb=" OE1 GLU A 291 "
     model   vdw
     2.449 2.752
  nonbonded pdb=" CB  GLU B 291 "
            pdb=" OE1 GLU B 291 "
     model   vdw
     2.449 2.752
  nonbonded pdb=" OE1 GLU B 291 "
            pdb=" OG1 THR B 539 "
     model   vdw
     2.501 3.040
  ... (remaining 60254 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:             1.790
  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:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.210
  Find NCS groups from input model:        0.050
  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:1.340
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
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      :  0.020   0.153   7352  Z= 1.044
  Angle     :  1.425  13.192  10006  Z= 0.978
  Chirality :  0.091   0.347   1170
  Planarity :  0.014   0.150   1224
  Dihedral  : 10.542  86.142   2546
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 1.72
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  2.82 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  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: -0.30 (0.25), residues: 922
  helix:  0.29 (0.18), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.27 (0.40), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 338 
 TYR   0.044   0.010   TYR B 296 
 PHE   0.029   0.005   PHE A 547 
 TRP   0.017   0.005   TRP A 322 
 HIS   0.007   0.002   HIS B 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.02031 ( 7352)
  covalent geometry    : angle       1.42545 (10006)
  hydrogen bonds       : bond        0.17340 (  551)
  hydrogen bonds       : angle       6.39986 ( 1551)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0475
  time to fit residues: 8.8316
Evaluate side-chains
  82 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 369 HIS
A 436 HIS
B 369 HIS
B 436 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.118855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.102520 restraints weight = 8661.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3029 rms_B_bonded: 1.73
r_work: 0.2931 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2799 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7352  Z= 0.183
  Angle     :  0.619   6.086  10006  Z= 0.334
  Chirality :  0.044   0.151   1170
  Planarity :  0.008   0.072   1224
  Dihedral  :  4.186  15.548    978
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  :  5.25 %
    Favored  : 92.91 %
  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 (0.28), residues: 922
  helix:  1.98 (0.19), residues: 672
  sheet:  None (None), residues: 0
  loop : -0.80 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 317 
 TYR   0.010   0.001   TYR B 589 
 PHE   0.030   0.002   PHE A 547 
 TRP   0.013   0.001   TRP B 469 
 HIS   0.004   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 7352)
  covalent geometry    : angle       0.61938 (10006)
  hydrogen bonds       : bond        0.06278 (  551)
  hydrogen bonds       : angle       4.47823 ( 1551)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  325 ASP cc_start: 0.8307 (t0) cc_final: 0.7858 (t0)
REVERT: A  346 LYS cc_start: 0.8182 (mttt) cc_final: 0.7590 (mptt)
REVERT: A  466 MET cc_start: 0.7463 (mmt) cc_final: 0.7201 (mmt)
REVERT: A  583 GLN cc_start: 0.6899 (mt0) cc_final: 0.6666 (tt0)
REVERT: B  325 ASP cc_start: 0.8317 (t0) cc_final: 0.7871 (t0)
REVERT: B  346 LYS cc_start: 0.8180 (mttt) cc_final: 0.7593 (mptt)
REVERT: B  466 MET cc_start: 0.7459 (mmt) cc_final: 0.7199 (mmt)
REVERT: B  583 GLN cc_start: 0.6923 (mt0) cc_final: 0.6685 (tt0)
  outliers start: 14
  outliers final: 10
  residues processed: 134
  average time/residue: 0.0542
  time to fit residues: 10.7593
Evaluate side-chains
  114 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  189 SER
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  410 MET
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  410 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 70 optimal weight:    0.5980
   chunk 88 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 60 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9980
   chunk 85 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9980
   chunk 40 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.118927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.102096 restraints weight = 8613.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 1.82
r_work: 0.2924 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2792 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7352  Z= 0.162
  Angle     :  0.547   6.215  10006  Z= 0.292
  Chirality :  0.042   0.143   1170
  Planarity :  0.006   0.064   1224
  Dihedral  :  3.866  13.770    978
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  :  7.87 %
    Favored  : 89.76 %
  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:  2.53 (0.28), residues: 922
  helix:  2.53 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -0.68 (0.41), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 496 
 TYR   0.008   0.001   TYR B 137 
 PHE   0.029   0.002   PHE A 547 
 TRP   0.014   0.001   TRP B 469 
 HIS   0.002   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 7352)
  covalent geometry    : angle       0.54675 (10006)
  hydrogen bonds       : bond        0.05457 (  551)
  hydrogen bonds       : angle       4.14203 ( 1551)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  295 THR cc_start: 0.8991 (m) cc_final: 0.8617 (t)
REVERT: A  325 ASP cc_start: 0.8559 (t0) cc_final: 0.8144 (t0)
REVERT: A  346 LYS cc_start: 0.8072 (mttt) cc_final: 0.7562 (mptt)
REVERT: A  466 MET cc_start: 0.7521 (mmt) cc_final: 0.7262 (mmt)
REVERT: A  583 GLN cc_start: 0.7228 (mt0) cc_final: 0.6929 (tt0)
REVERT: B  295 THR cc_start: 0.8982 (m) cc_final: 0.8607 (t)
REVERT: B  325 ASP cc_start: 0.8569 (t0) cc_final: 0.8144 (t0)
REVERT: B  346 LYS cc_start: 0.8073 (mttt) cc_final: 0.7562 (mptt)
REVERT: B  466 MET cc_start: 0.7531 (mmt) cc_final: 0.7270 (mmt)
REVERT: B  583 GLN cc_start: 0.7231 (mt0) cc_final: 0.6932 (tt0)
  outliers start: 18
  outliers final: 12
  residues processed: 118
  average time/residue: 0.0540
  time to fit residues: 9.5315
Evaluate side-chains
  112 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  410 MET
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  540 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 75 optimal weight:    0.0070
   chunk 72 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 73 optimal weight:    0.4980
   chunk 20 optimal weight:    3.9990
   overall best weight:    0.8000

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.117692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.100785 restraints weight = 8729.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 1.82
r_work: 0.2905 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.2786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7352  Z= 0.165
  Angle     :  0.547   6.089  10006  Z= 0.287
  Chirality :  0.042   0.142   1170
  Planarity :  0.006   0.066   1224
  Dihedral  :  3.815  13.630    978
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  :  7.87 %
    Favored  : 89.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.54 (0.28), residues: 922
  helix:  2.56 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.78 (0.40), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 377 
 TYR   0.009   0.001   TYR B 146 
 PHE   0.029   0.002   PHE A 547 
 TRP   0.014   0.001   TRP B 469 
 HIS   0.003   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 7352)
  covalent geometry    : angle       0.54678 (10006)
  hydrogen bonds       : bond        0.05324 (  551)
  hydrogen bonds       : angle       4.08780 ( 1551)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 LYS cc_start: 0.7497 (ttpp) cc_final: 0.6994 (ptmm)
REVERT: A  295 THR cc_start: 0.8903 (m) cc_final: 0.8582 (t)
REVERT: A  325 ASP cc_start: 0.8513 (t0) cc_final: 0.8063 (t0)
REVERT: A  346 LYS cc_start: 0.8074 (mttt) cc_final: 0.7603 (mptt)
REVERT: A  410 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7559 (ttt)
REVERT: A  583 GLN cc_start: 0.7221 (mt0) cc_final: 0.6889 (tt0)
REVERT: B  204 LYS cc_start: 0.7487 (ttpp) cc_final: 0.6986 (ptmm)
REVERT: B  295 THR cc_start: 0.8896 (m) cc_final: 0.8576 (t)
REVERT: B  325 ASP cc_start: 0.8522 (t0) cc_final: 0.8064 (t0)
REVERT: B  346 LYS cc_start: 0.8070 (mttt) cc_final: 0.7598 (mptt)
REVERT: B  410 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7548 (ttt)
REVERT: B  583 GLN cc_start: 0.7207 (mt0) cc_final: 0.6874 (tt0)
  outliers start: 20
  outliers final: 16
  residues processed: 120
  average time/residue: 0.0602
  time to fit residues: 10.7923
Evaluate side-chains
  134 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  189 SER
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  410 MET
Chi-restraints excluded: chain A residue  502 MET
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  502 MET
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  540 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 26 optimal weight:    0.3980
   chunk 38 optimal weight:    3.9990
   chunk 10 optimal weight:    0.2980
   chunk 64 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 88 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.119427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.102299 restraints weight = 8731.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 1.84
r_work: 0.2928 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2795 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.3006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7352  Z= 0.138
  Angle     :  0.511   5.637  10006  Z= 0.269
  Chirality :  0.041   0.145   1170
  Planarity :  0.006   0.060   1224
  Dihedral  :  3.722  14.037    978
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  :  9.19 %
    Favored  : 88.45 %
  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:  2.81 (0.28), residues: 922
  helix:  2.77 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.72 (0.40), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 377 
 TYR   0.008   0.001   TYR B 137 
 PHE   0.028   0.001   PHE A 547 
 TRP   0.015   0.001   TRP A 469 
 HIS   0.002   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 7352)
  covalent geometry    : angle       0.51075 (10006)
  hydrogen bonds       : bond        0.04848 (  551)
  hydrogen bonds       : angle       3.99862 ( 1551)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 LYS cc_start: 0.7423 (ttpp) cc_final: 0.7032 (ptmm)
REVERT: A  295 THR cc_start: 0.8948 (m) cc_final: 0.8611 (t)
REVERT: A  325 ASP cc_start: 0.8522 (t0) cc_final: 0.8040 (t0)
REVERT: A  346 LYS cc_start: 0.8034 (mttt) cc_final: 0.7591 (mptt)
REVERT: A  583 GLN cc_start: 0.7224 (mt0) cc_final: 0.6857 (tt0)
REVERT: B  204 LYS cc_start: 0.7427 (ttpp) cc_final: 0.7039 (ptmm)
REVERT: B  295 THR cc_start: 0.8947 (m) cc_final: 0.8608 (t)
REVERT: B  325 ASP cc_start: 0.8521 (t0) cc_final: 0.8042 (t0)
REVERT: B  346 LYS cc_start: 0.8029 (mttt) cc_final: 0.7585 (mptt)
REVERT: B  583 GLN cc_start: 0.7221 (mt0) cc_final: 0.6850 (tt0)
  outliers start: 18
  outliers final: 16
  residues processed: 130
  average time/residue: 0.0708
  time to fit residues: 13.1101
Evaluate side-chains
  130 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  189 SER
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  502 MET
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  477 MET
Chi-restraints excluded: chain B residue  502 MET
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  540 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 30 optimal weight:    0.0970
   chunk 18 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 90 optimal weight:    0.4980
   chunk 64 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 85 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.3224 r_free = 0.3224 target = 0.119002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.101726 restraints weight = 8705.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 1.87
r_work: 0.2915 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2781 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.3152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7352  Z= 0.138
  Angle     :  0.516   5.617  10006  Z= 0.268
  Chirality :  0.041   0.143   1170
  Planarity :  0.006   0.061   1224
  Dihedral  :  3.652  14.275    978
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  :  8.66 %
    Favored  : 87.93 %
  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:  2.78 (0.28), residues: 922
  helix:  2.77 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.78 (0.40), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 377 
 TYR   0.007   0.001   TYR B 137 
 PHE   0.028   0.001   PHE B 547 
 TRP   0.014   0.001   TRP A 469 
 HIS   0.002   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 7352)
  covalent geometry    : angle       0.51578 (10006)
  hydrogen bonds       : bond        0.04756 (  551)
  hydrogen bonds       : angle       3.95858 ( 1551)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 110
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7563 (t80)
REVERT: A  325 ASP cc_start: 0.8630 (t0) cc_final: 0.8183 (t0)
REVERT: A  346 LYS cc_start: 0.8076 (mttt) cc_final: 0.7638 (mptt)
REVERT: A  410 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7579 (ttt)
REVERT: A  583 GLN cc_start: 0.7329 (mt0) cc_final: 0.6956 (tt0)
REVERT: B  235 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7580 (t80)
REVERT: B  325 ASP cc_start: 0.8637 (t0) cc_final: 0.8197 (t0)
REVERT: B  346 LYS cc_start: 0.8071 (mttt) cc_final: 0.7636 (mptt)
REVERT: B  410 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7577 (ttt)
REVERT: B  583 GLN cc_start: 0.7333 (mt0) cc_final: 0.6955 (tt0)
  outliers start: 26
  outliers final: 20
  residues processed: 126
  average time/residue: 0.0513
  time to fit residues: 9.7416
Evaluate side-chains
  133 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  410 MET
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  502 MET
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  262 TYR
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  457 VAL
Chi-restraints excluded: chain B residue  477 MET
Chi-restraints excluded: chain B residue  502 MET
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  547 PHE
Chi-restraints excluded: chain B residue  556 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 78 optimal weight:    0.2980
   chunk 9 optimal weight:    0.6980
   chunk 66 optimal weight:    0.1980
   chunk 2 optimal weight:    0.6980
   chunk 90 optimal weight:    0.8980
   chunk 88 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3236 r_free = 0.3236 target = 0.120001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.102683 restraints weight = 8693.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 1.86
r_work: 0.2932 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2800 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7352  Z= 0.130
  Angle     :  0.497   5.569  10006  Z= 0.260
  Chirality :  0.040   0.143   1170
  Planarity :  0.006   0.058   1224
  Dihedral  :  3.578  14.160    978
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  :  9.58 %
    Favored  : 87.27 %
  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:  2.91 (0.28), residues: 922
  helix:  2.85 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.70 (0.40), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 377 
 TYR   0.007   0.001   TYR B 137 
 PHE   0.027   0.001   PHE A 547 
 TRP   0.015   0.001   TRP A 469 
 HIS   0.002   0.001   HIS B 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7352)
  covalent geometry    : angle       0.49720 (10006)
  hydrogen bonds       : bond        0.04511 (  551)
  hydrogen bonds       : angle       3.90090 ( 1551)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7550 (t80)
REVERT: A  325 ASP cc_start: 0.8615 (t0) cc_final: 0.8157 (t0)
REVERT: A  410 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7404 (ttt)
REVERT: A  419 MET cc_start: 0.8202 (mmt) cc_final: 0.7995 (mmp)
REVERT: A  583 GLN cc_start: 0.7264 (mt0) cc_final: 0.6886 (tt0)
REVERT: B  235 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7632 (t80)
REVERT: B  325 ASP cc_start: 0.8627 (t0) cc_final: 0.8175 (t0)
REVERT: B  410 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7397 (ttt)
REVERT: B  583 GLN cc_start: 0.7259 (mt0) cc_final: 0.6876 (tt0)
  outliers start: 24
  outliers final: 20
  residues processed: 125
  average time/residue: 0.0531
  time to fit residues: 10.0363
Evaluate side-chains
  132 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  339 MET
Chi-restraints excluded: chain A residue  410 MET
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  502 MET
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  262 TYR
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  339 MET
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  457 VAL
Chi-restraints excluded: chain B residue  502 MET
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  547 PHE
Chi-restraints excluded: chain B residue  556 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 90 optimal weight:    0.4980
   chunk 70 optimal weight:    0.6980
   chunk 67 optimal weight:    0.0060
   chunk 60 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 87 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
A 574 GLN
B 574 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.119934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.102559 restraints weight = 8724.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 1.85
r_work: 0.2934 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2802 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.3370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7352  Z= 0.132
  Angle     :  0.521   6.457  10006  Z= 0.267
  Chirality :  0.041   0.141   1170
  Planarity :  0.006   0.059   1224
  Dihedral  :  3.551  15.573    978
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 10.37 %
    Favored  : 86.22 %
  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:  2.91 (0.28), residues: 922
  helix:  2.85 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.67 (0.41), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 199 
 TYR   0.007   0.001   TYR B 137 
 PHE   0.027   0.001   PHE B 547 
 TRP   0.014   0.001   TRP A 469 
 HIS   0.002   0.001   HIS B 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 7352)
  covalent geometry    : angle       0.52059 (10006)
  hydrogen bonds       : bond        0.04522 (  551)
  hydrogen bonds       : angle       3.88670 ( 1551)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7671 (t80)
REVERT: A  325 ASP cc_start: 0.8613 (t0) cc_final: 0.8136 (t0)
REVERT: A  410 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7431 (ttt)
REVERT: A  419 MET cc_start: 0.8246 (mmt) cc_final: 0.8042 (mmp)
REVERT: A  583 GLN cc_start: 0.7305 (mt0) cc_final: 0.6916 (tt0)
REVERT: B  235 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7672 (t80)
REVERT: B  325 ASP cc_start: 0.8638 (t0) cc_final: 0.8168 (t0)
REVERT: B  410 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7445 (ttt)
REVERT: B  583 GLN cc_start: 0.7295 (mt0) cc_final: 0.6902 (tt0)
  outliers start: 26
  outliers final: 22
  residues processed: 125
  average time/residue: 0.0568
  time to fit residues: 11.0349
Evaluate side-chains
  128 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  339 MET
Chi-restraints excluded: chain A residue  410 MET
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  502 MET
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  262 TYR
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  339 MET
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  457 VAL
Chi-restraints excluded: chain B residue  477 MET
Chi-restraints excluded: chain B residue  502 MET
Chi-restraints excluded: chain B residue  516 ILE
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  547 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 39 optimal weight:    0.3980
   chunk 85 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 21 optimal weight:    0.2980
   chunk 19 optimal weight:    1.9990
   chunk 22 optimal weight:    0.4980
   chunk 26 optimal weight:    0.3980
   chunk 69 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.3247 r_free = 0.3247 target = 0.120856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.103475 restraints weight = 8616.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 1.83
r_work: 0.2947 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2816 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.3473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7352  Z= 0.126
  Angle     :  0.516   7.187  10006  Z= 0.263
  Chirality :  0.040   0.141   1170
  Planarity :  0.006   0.058   1224
  Dihedral  :  3.492  15.173    978
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 10.24 %
    Favored  : 86.09 %
  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:  3.03 (0.28), residues: 922
  helix:  2.92 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.59 (0.42), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 377 
 TYR   0.007   0.001   TYR A 137 
 PHE   0.027   0.001   PHE B 547 
 TRP   0.014   0.001   TRP B 469 
 HIS   0.002   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 7352)
  covalent geometry    : angle       0.51625 (10006)
  hydrogen bonds       : bond        0.04388 (  551)
  hydrogen bonds       : angle       3.85718 ( 1551)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7616 (t80)
REVERT: A  325 ASP cc_start: 0.8655 (t0) cc_final: 0.8193 (t0)
REVERT: A  410 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7408 (ttt)
REVERT: A  419 MET cc_start: 0.8219 (mmt) cc_final: 0.8008 (mmp)
REVERT: A  583 GLN cc_start: 0.7276 (mt0) cc_final: 0.6885 (tt0)
REVERT: B  235 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7636 (t80)
REVERT: B  325 ASP cc_start: 0.8660 (t0) cc_final: 0.8212 (t0)
REVERT: B  410 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7406 (ttt)
REVERT: B  583 GLN cc_start: 0.7271 (mt0) cc_final: 0.6872 (tt0)
  outliers start: 28
  outliers final: 22
  residues processed: 119
  average time/residue: 0.0527
  time to fit residues: 9.7271
Evaluate side-chains
  131 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 105
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  339 MET
Chi-restraints excluded: chain A residue  410 MET
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  502 MET
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  262 TYR
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  339 MET
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  457 VAL
Chi-restraints excluded: chain B residue  477 MET
Chi-restraints excluded: chain B residue  502 MET
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  547 PHE
Chi-restraints excluded: chain B residue  556 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 69 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 82 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 72 optimal weight:    0.0570
   chunk 19 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.5898

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.120005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.102376 restraints weight = 8708.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 1.88
r_work: 0.2926 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2795 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.3465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7352  Z= 0.136
  Angle     :  0.527   7.754  10006  Z= 0.268
  Chirality :  0.041   0.139   1170
  Planarity :  0.006   0.058   1224
  Dihedral  :  3.502  15.247    978
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 10.76 %
    Favored  : 85.83 %
  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:  2.94 (0.28), residues: 922
  helix:  2.86 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.63 (0.41), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 377 
 TYR   0.007   0.001   TYR A 137 
 PHE   0.028   0.001   PHE B 547 
 TRP   0.013   0.001   TRP A 469 
 HIS   0.002   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 7352)
  covalent geometry    : angle       0.52726 (10006)
  hydrogen bonds       : bond        0.04569 (  551)
  hydrogen bonds       : angle       3.87185 ( 1551)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7676 (t80)
REVERT: A  325 ASP cc_start: 0.8654 (t0) cc_final: 0.8170 (t0)
REVERT: A  410 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7479 (ttt)
REVERT: A  419 MET cc_start: 0.8272 (mmt) cc_final: 0.8062 (mmp)
REVERT: A  583 GLN cc_start: 0.7331 (mt0) cc_final: 0.6919 (tt0)
REVERT: B  235 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7703 (t80)
REVERT: B  325 ASP cc_start: 0.8688 (t0) cc_final: 0.8221 (t0)
REVERT: B  410 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7490 (ttt)
REVERT: B  583 GLN cc_start: 0.7320 (mt0) cc_final: 0.6901 (tt0)
  outliers start: 26
  outliers final: 22
  residues processed: 125
  average time/residue: 0.0529
  time to fit residues: 10.2606
Evaluate side-chains
  135 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  339 MET
Chi-restraints excluded: chain A residue  410 MET
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  502 MET
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  262 TYR
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  339 MET
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  457 VAL
Chi-restraints excluded: chain B residue  477 MET
Chi-restraints excluded: chain B residue  502 MET
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  547 PHE
Chi-restraints excluded: chain B residue  556 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 90 optimal weight:    0.0050
   chunk 43 optimal weight:    0.9990
   chunk 89 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 83 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.5994

-------------------------------------------------------------------------------
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 = 0.3232 r_free = 0.3232 target = 0.119671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.102363 restraints weight = 8692.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3032 rms_B_bonded: 1.85
r_work: 0.2930 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2799 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.3510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7352  Z= 0.138
  Angle     :  0.534   7.839  10006  Z= 0.272
  Chirality :  0.041   0.139   1170
  Planarity :  0.006   0.057   1224
  Dihedral  :  3.501  15.164    978
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 10.76 %
    Favored  : 85.83 %
  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:  2.94 (0.28), residues: 922
  helix:  2.85 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.62 (0.42), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 377 
 TYR   0.007   0.001   TYR B 137 
 PHE   0.027   0.001   PHE A 547 
 TRP   0.014   0.001   TRP B 469 
 HIS   0.002   0.001   HIS B 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 7352)
  covalent geometry    : angle       0.53414 (10006)
  hydrogen bonds       : bond        0.04628 (  551)
  hydrogen bonds       : angle       3.89005 ( 1551)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1507.46 seconds
wall clock time: 26 minutes 31.37 seconds (1591.37 seconds total)