Starting phenix.real_space_refine
on Wed Sep 17 03:15:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xiu_38390/09_2025/8xiu_38390.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xiu_38390/09_2025/8xiu_38390.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xiu_38390/09_2025/8xiu_38390.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xiu_38390/09_2025/8xiu_38390.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xiu_38390/09_2025/8xiu_38390.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xiu_38390/09_2025/8xiu_38390.cif"
  }
  resolution = 4.0
  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=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    1745      2.51       5
     N     401      2.21       5
     O     439      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2615
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 348, 2615
          Classifications: {'peptide': 348}
          Link IDs: {'PTRANS': 18, 'TRANS': 329}
          Chain breaks: 5
  Time building chain proxies: 0.86, per 1000 atoms: 0.33
  Number of scatterers: 2615
  At special positions: 0
  Unit cell: (72.25, 57.8, 69.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O     439      8.00
     N     401      7.00
     C    1745      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: 0.22
  Conformation dependent library (CDL) restraints added in 115.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  628

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 0 sheets defined
      89.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 39
      removed outlier: 3.930A  pdb=" N   LEU A  23 " --> pdb=" O   ARG A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 49
      removed outlier: 3.689A  pdb=" N   TYR A  49 " --> pdb=" O   PRO A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 155
      removed outlier: 3.849A  pdb=" N   PHE A 134 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
      removed outlier: 4.616A  pdb=" N   LYS A 137 " --> pdb=" O   LEU A 133 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   ALA A 138 " --> pdb=" O   PHE A 134 " (cutoff:3.500A)
      Proline residue:  A 146  - end of helix
      Proline residue:  A 150  - end of helix
      removed outlier: 4.086A  pdb=" N   ASN A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 173
      removed outlier: 4.099A  pdb=" N   ILE A 173 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 177
    Processing helix  chain 'A' and resid 180 through 210
      removed outlier: 3.541A  pdb=" N   TYR A 210 " --> pdb=" O   LEU A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 244
      Proline residue:  A 235  - end of helix
      removed outlier: 4.126A  pdb=" N   GLU A 243 " --> pdb=" O   SER A 239 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   PHE A 244 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 269
      removed outlier: 4.111A  pdb=" N   LEU A 259 " --> pdb=" O   ALA A 255 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   PHE A 260 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ASP A 261 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU A 269 " --> pdb=" O   GLN A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 322
      removed outlier: 3.865A  pdb=" N   LEU A 294 " --> pdb=" O   ASP A 290 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   ALA A 296 " --> pdb=" O   TYR A 292 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   ILE A 307 " --> pdb=" O   ALA A 303 " (cutoff:3.500A)
      Proline residue:  A 312  - end of helix
      Proline residue:  A 315  - end of helix
    Processing helix  chain 'A' and resid 333 through 348
      removed outlier: 4.054A  pdb=" N   ASN A 345 " --> pdb=" O   LEU A 341 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   ILE A 346 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 355 through 374
      removed outlier: 4.379A  pdb=" N   CYS A 359 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 383
    Processing helix  chain 'A' and resid 384 through 412
      removed outlier: 3.827A  pdb=" N   PHE A 388 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   GLY A 389 " --> pdb=" O   ALA A 385 " (cutoff:3.500A)
      Proline residue:  A 403  - end of helix
      removed outlier: 4.211A  pdb=" N   GLY A 406 " --> pdb=" O   MET A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 435
      removed outlier: 4.357A  pdb=" N   GLY A 431 " --> pdb=" O   ALA A 427 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   PHE A 432 " --> pdb=" O   PHE A 428 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   PHE A 434 " --> pdb=" O   MET A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 445
    Processing helix  chain 'A' and resid 454 through 463
      removed outlier: 3.503A  pdb=" N   VAL A 458 " --> pdb=" O   ILE A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 468
      removed outlier: 4.448A  pdb=" N   PHE A 468 " --> pdb=" O   LEU A 465 " (cutoff:3.500A)

    196 hydrogen bonds defined for protein.
    573 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.38

  Time building geometry restraints manager: 0.31 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 779
        1.35 -     1.46: 616
        1.46 -     1.58: 1225
        1.58 -     1.69: 0
        1.69 -     1.81: 53
  Bond restraints: 2673
  Sorted by residual:
  bond pdb=" C   VAL A 374 "
       pdb=" N   PRO A 375 "
    ideal  model  delta    sigma   weight residual
    1.335  1.345 -0.010 1.30e-02 5.92e+03 5.73e-01
  bond pdb=" C   PRO A 235 "
       pdb=" N   PRO A 236 "
    ideal  model  delta    sigma   weight residual
    1.336  1.344 -0.008 1.20e-02 6.94e+03 4.26e-01
  bond pdb=" CA  ASN A 145 "
       pdb=" C   ASN A 145 "
    ideal  model  delta    sigma   weight residual
    1.520  1.528 -0.008 1.23e-02 6.61e+03 4.02e-01
  bond pdb=" C   LEU A 314 "
       pdb=" N   PRO A 315 "
    ideal  model  delta    sigma   weight residual
    1.335  1.343 -0.008 1.28e-02 6.10e+03 3.90e-01
  bond pdb=" CA  MET A 402 "
       pdb=" C   MET A 402 "
    ideal  model  delta    sigma   weight residual
    1.520  1.528 -0.008 1.23e-02 6.61e+03 3.72e-01
  ... (remaining 2668 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 3539
        1.41 -     2.82: 66
        2.82 -     4.23: 12
        4.23 -     5.64: 7
        5.64 -     7.05: 3
  Bond angle restraints: 3627
  Sorted by residual:
  angle pdb=" N   PRO A 235 "
        pdb=" CA  PRO A 235 "
        pdb=" C   PRO A 235 "
      ideal   model   delta    sigma   weight residual
     110.70  113.20   -2.50 1.22e+00 6.72e-01 4.19e+00
  angle pdb=" CA  PRO A 235 "
        pdb=" C   PRO A 235 "
        pdb=" N   PRO A 236 "
      ideal   model   delta    sigma   weight residual
     117.93  120.28   -2.35 1.20e+00 6.94e-01 3.82e+00
  angle pdb=" C   PRO A 235 "
        pdb=" N   PRO A 236 "
        pdb=" CD  PRO A 236 "
      ideal   model   delta    sigma   weight residual
     125.00  132.05   -7.05 4.10e+00 5.95e-02 2.96e+00
  angle pdb=" CA  LEU A 461 "
        pdb=" CB  LEU A 461 "
        pdb=" CG  LEU A 461 "
      ideal   model   delta    sigma   weight residual
     116.30  122.02   -5.72 3.50e+00 8.16e-02 2.67e+00
  angle pdb=" N   PHE A 434 "
        pdb=" CA  PHE A 434 "
        pdb=" C   PHE A 434 "
      ideal   model   delta    sigma   weight residual
     110.61  112.65   -2.04 1.25e+00 6.40e-01 2.66e+00
  ... (remaining 3622 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.17: 1417
       11.17 -    22.35: 81
       22.35 -    33.52: 34
       33.52 -    44.69: 19
       44.69 -    55.86: 6
  Dihedral angle restraints: 1557
    sinusoidal: 575
      harmonic: 982
  Sorted by residual:
  dihedral pdb=" CA  VAL A 374 "
           pdb=" C   VAL A 374 "
           pdb=" N   PRO A 375 "
           pdb=" CA  PRO A 375 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.18  -16.82     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CA  GLN A 141 "
           pdb=" CB  GLN A 141 "
           pdb=" CG  GLN A 141 "
           pdb=" CD  GLN A 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -124.14  -55.86     3      1.50e+01 4.44e-03 9.37e+00
  dihedral pdb=" N   TYR A 157 "
           pdb=" CA  TYR A 157 "
           pdb=" CB  TYR A 157 "
           pdb=" CG  TYR A 157 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   -6.46  -53.54     3      1.50e+01 4.44e-03 9.21e+00
  ... (remaining 1554 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 267
       0.026 -    0.053: 96
       0.053 -    0.079: 42
       0.079 -    0.106: 24
       0.106 -    0.132: 8
  Chirality restraints: 437
  Sorted by residual:
  chirality pdb=" CA  VAL A 374 "
            pdb=" N   VAL A 374 "
            pdb=" C   VAL A 374 "
            pdb=" CB  VAL A 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.31    0.13 2.00e-01 2.50e+01 4.37e-01
  chirality pdb=" CA  ILE A  44 "
            pdb=" N   ILE A  44 "
            pdb=" C   ILE A  44 "
            pdb=" CB  ILE A  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.76e-01
  chirality pdb=" CA  MET A 402 "
            pdb=" N   MET A 402 "
            pdb=" C   MET A 402 "
            pdb=" CB  MET A 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.48e-01
  ... (remaining 434 not shown)

  Planarity restraints: 441
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 234 "    0.031 5.00e-02 4.00e+02   4.67e-02 3.49e+00
        pdb=" N   PRO A 235 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 235 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 235 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 159 "    0.028 5.00e-02 4.00e+02   4.25e-02 2.89e+00
        pdb=" N   PRO A 160 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 160 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 160 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A  44 "   -0.025 5.00e-02 4.00e+02   3.83e-02 2.35e+00
        pdb=" N   PRO A  45 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A  45 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A  45 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 438 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 898
        2.87 -     3.37: 2904
        3.37 -     3.88: 4170
        3.88 -     4.39: 4163
        4.39 -     4.90: 7407
  Nonbonded interactions: 19542
  Sorted by model distance:
  nonbonded pdb=" O   TRP A 317 "
            pdb=" OG1 THR A 321 "
     model   vdw
     2.357 3.040
  nonbonded pdb=" OG  SER A 339 "
            pdb=" O   PHE A 388 "
     model   vdw
     2.379 3.040
  nonbonded pdb=" N   ASP A 213 "
            pdb=" OD1 ASP A 213 "
     model   vdw
     2.411 3.120
  nonbonded pdb=" O   TYR A 210 "
            pdb=" NE  ARG A 216 "
     model   vdw
     2.469 3.120
  nonbonded pdb=" O   VAL A 140 "
            pdb=" OG1 THR A 144 "
     model   vdw
     2.480 3.040
  ... (remaining 19537 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     4.610
  Find NCS groups from input model:        0.010
  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:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7030
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      :  0.002   0.022   2673  Z= 0.110
  Angle     :  0.554   7.054   3627  Z= 0.277
  Chirality :  0.039   0.132    437
  Planarity :  0.005   0.047    441
  Dihedral  : 10.636  55.863    929
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 11.83 %
    Favored  : 87.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.65 (0.48), residues: 336
  helix:  2.30 (0.33), residues: 274
  sheet:  None (None), residues: 0
  loop : -0.79 (0.83), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  19 
 TYR   0.007   0.001   TYR A 340 
 PHE   0.010   0.001   PHE A 134 
 TRP   0.003   0.001   TRP A 317 
 HIS   0.001   0.000   HIS A 413 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 2673)
  covalent geometry    : angle       0.55441 ( 3627)
  hydrogen bonds       : bond        0.08270 (  196)
  hydrogen bonds       : angle       3.80347 (  573)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 104
  time to evaluate  : 0.097 
Fit side-chains
REVERT: A   20 LYS cc_start: 0.6381 (mtmt) cc_final: 0.6093 (mtmm)
REVERT: A  157 TYR cc_start: 0.6751 (OUTLIER) cc_final: 0.6530 (m-80)
REVERT: A  168 MET cc_start: 0.8309 (mmt) cc_final: 0.7958 (mmt)
REVERT: A  229 MET cc_start: 0.8948 (mtp) cc_final: 0.8541 (mmt)
REVERT: A  309 MET cc_start: 0.8693 (tpp) cc_final: 0.8482 (tpp)
REVERT: A  341 LEU cc_start: 0.8797 (tp) cc_final: 0.8493 (tp)
REVERT: A  364 MET cc_start: 0.7739 (mtp) cc_final: 0.7428 (mtm)
REVERT: A  401 MET cc_start: 0.7252 (ttm) cc_final: 0.6760 (ttm)
REVERT: A  428 PHE cc_start: 0.8264 (t80) cc_final: 0.7692 (t80)
  outliers start: 3
  outliers final: 2
  residues processed: 105
  average time/residue: 0.0506
  time to fit residues: 6.4353
Evaluate side-chains
  90 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  165 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.3980
   chunk 16 optimal weight:    0.0970
   chunk 32 optimal weight:    0.2980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.3978

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

Flipped N/Q/H residues before XYZ refinement:
A 265 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.166615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.152497 restraints weight = 6835.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.155951 restraints weight = 4151.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.158567 restraints weight = 2782.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.160342 restraints weight = 1922.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.161409 restraints weight = 1387.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.4016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2673  Z= 0.125
  Angle     :  0.653   9.842   3627  Z= 0.305
  Chirality :  0.041   0.138    437
  Planarity :  0.006   0.053    441
  Dihedral  :  5.307  52.453    369
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 20.43 %
    Favored  : 75.27 %
  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:  2.35 (0.48), residues: 336
  helix:  2.05 (0.32), residues: 276
  sheet:  None (None), residues: 0
  loop : -0.74 (0.82), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 378 
 TYR   0.011   0.001   TYR A 421 
 PHE   0.025   0.001   PHE A 237 
 TRP   0.002   0.000   TRP A 317 
 HIS   0.007   0.002   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 2673)
  covalent geometry    : angle       0.65268 ( 3627)
  hydrogen bonds       : bond        0.03472 (  196)
  hydrogen bonds       : angle       3.78587 (  573)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A  157 TYR cc_start: 0.6867 (OUTLIER) cc_final: 0.6586 (m-80)
REVERT: A  229 MET cc_start: 0.8934 (mtp) cc_final: 0.8586 (mmt)
REVERT: A  341 LEU cc_start: 0.8826 (tp) cc_final: 0.8608 (tp)
REVERT: A  364 MET cc_start: 0.7442 (mtp) cc_final: 0.7233 (mtm)
REVERT: A  428 PHE cc_start: 0.8121 (t80) cc_final: 0.7630 (t80)
  outliers start: 12
  outliers final: 8
  residues processed: 96
  average time/residue: 0.0349
  time to fit residues: 4.3337
Evaluate side-chains
  95 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  161 MET
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  357 TRP
Chi-restraints excluded: chain A residue  465 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0970
   chunk 32 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 10 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4052 r_free = 0.4052 target = 0.163945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.149254 restraints weight = 6627.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.152838 restraints weight = 4055.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.155243 restraints weight = 2676.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.156881 restraints weight = 1892.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.157975 restraints weight = 1395.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7150
moved from start:          0.1924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2673  Z= 0.127
  Angle     :  0.645   9.096   3627  Z= 0.304
  Chirality :  0.041   0.118    437
  Planarity :  0.006   0.055    441
  Dihedral  :  5.335  50.794    369
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 22.22 %
    Favored  : 73.12 %
  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:  2.06 (0.48), residues: 336
  helix:  1.80 (0.32), residues: 281
  sheet:  None (None), residues: 0
  loop : -0.85 (0.87), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 378 
 TYR   0.011   0.001   TYR A  47 
 PHE   0.021   0.001   PHE A 237 
 TRP   0.002   0.001   TRP A 450 
 HIS   0.005   0.002   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 2673)
  covalent geometry    : angle       0.64502 ( 3627)
  hydrogen bonds       : bond        0.03561 (  196)
  hydrogen bonds       : angle       3.87393 (  573)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.094 
Fit side-chains
REVERT: A  157 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.6618 (m-80)
REVERT: A  229 MET cc_start: 0.8966 (mtp) cc_final: 0.8583 (mmt)
REVERT: A  364 MET cc_start: 0.7543 (mtp) cc_final: 0.7225 (mtm)
REVERT: A  428 PHE cc_start: 0.8204 (t80) cc_final: 0.7969 (t80)
  outliers start: 13
  outliers final: 10
  residues processed: 95
  average time/residue: 0.0447
  time to fit residues: 5.3156
Evaluate side-chains
  99 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  161 MET
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  357 TRP
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  465 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0980
   chunk 8 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.7384

-------------------------------------------------------------------------------
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 = 0.4063 r_free = 0.4063 target = 0.164849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.150655 restraints weight = 6787.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.153905 restraints weight = 4210.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.156389 restraints weight = 2875.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.157969 restraints weight = 2025.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.159135 restraints weight = 1511.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2673  Z= 0.133
  Angle     :  0.657   9.497   3627  Z= 0.312
  Chirality :  0.042   0.118    437
  Planarity :  0.006   0.055    441
  Dihedral  :  5.433  49.251    369
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 23.66 %
    Favored  : 71.68 %
  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:  1.92 (0.47), residues: 336
  helix:  1.79 (0.32), residues: 269
  sheet:  None (None), residues: 0
  loop : -0.77 (0.73), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 188 
 TYR   0.009   0.001   TYR A 421 
 PHE   0.019   0.001   PHE A 237 
 TRP   0.004   0.001   TRP A 450 
 HIS   0.003   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 2673)
  covalent geometry    : angle       0.65667 ( 3627)
  hydrogen bonds       : bond        0.03626 (  196)
  hydrogen bonds       : angle       3.94021 (  573)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.093 
Fit side-chains
REVERT: A  229 MET cc_start: 0.8949 (mtp) cc_final: 0.8688 (mmt)
REVERT: A  401 MET cc_start: 0.8171 (tpp) cc_final: 0.7962 (tpp)
REVERT: A  428 PHE cc_start: 0.8232 (t80) cc_final: 0.7778 (t80)
  outliers start: 13
  outliers final: 11
  residues processed: 94
  average time/residue: 0.0443
  time to fit residues: 5.1963
Evaluate side-chains
  96 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  161 MET
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  357 TRP
Chi-restraints excluded: chain A residue  465 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 304 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.164368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.150319 restraints weight = 6724.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.153742 restraints weight = 4050.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.156133 restraints weight = 2701.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.157715 restraints weight = 1883.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.158933 restraints weight = 1395.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.2466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2673  Z= 0.137
  Angle     :  0.649   9.054   3627  Z= 0.313
  Chirality :  0.042   0.122    437
  Planarity :  0.006   0.055    441
  Dihedral  :  4.882  45.648    367
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 24.37 %
    Favored  : 70.25 %
  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:  1.84 (0.47), residues: 336
  helix:  1.73 (0.32), residues: 269
  sheet:  None (None), residues: 0
  loop : -0.80 (0.72), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 188 
 TYR   0.011   0.001   TYR A  47 
 PHE   0.017   0.001   PHE A 237 
 TRP   0.004   0.001   TRP A 450 
 HIS   0.003   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 2673)
  covalent geometry    : angle       0.64925 ( 3627)
  hydrogen bonds       : bond        0.03837 (  196)
  hydrogen bonds       : angle       4.01113 (  573)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A  229 MET cc_start: 0.8976 (mtp) cc_final: 0.8546 (mmt)
  outliers start: 15
  outliers final: 14
  residues processed: 94
  average time/residue: 0.0437
  time to fit residues: 5.2119
Evaluate side-chains
  99 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  161 MET
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  357 TRP
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  465 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 18 optimal weight:    0.3980
   chunk 24 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 304 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.164784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.150738 restraints weight = 6658.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.154202 restraints weight = 4037.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.156516 restraints weight = 2641.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.158235 restraints weight = 1860.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.159195 restraints weight = 1359.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2673  Z= 0.137
  Angle     :  0.662   9.410   3627  Z= 0.322
  Chirality :  0.042   0.119    437
  Planarity :  0.006   0.058    441
  Dihedral  :  4.929  45.504    367
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 25.45 %
    Favored  : 69.18 %
  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 (0.47), residues: 336
  helix:  1.64 (0.32), residues: 269
  sheet:  None (None), residues: 0
  loop : -0.89 (0.72), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 188 
 TYR   0.009   0.001   TYR A 421 
 PHE   0.016   0.001   PHE A 237 
 TRP   0.005   0.001   TRP A 450 
 HIS   0.002   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 2673)
  covalent geometry    : angle       0.66235 ( 3627)
  hydrogen bonds       : bond        0.03898 (  196)
  hydrogen bonds       : angle       4.06224 (  573)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.109 
Fit side-chains
REVERT: A  229 MET cc_start: 0.8942 (mtp) cc_final: 0.8731 (mmt)
REVERT: A  340 TYR cc_start: 0.8045 (t80) cc_final: 0.7796 (t80)
REVERT: A  428 PHE cc_start: 0.8287 (t80) cc_final: 0.8036 (t80)
  outliers start: 15
  outliers final: 14
  residues processed: 98
  average time/residue: 0.0449
  time to fit residues: 5.4628
Evaluate side-chains
  98 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  357 TRP
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  388 PHE
Chi-restraints excluded: chain A residue  465 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0970
   chunk 7 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A 304 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.166616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.152532 restraints weight = 6734.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.155943 restraints weight = 4093.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.158017 restraints weight = 2705.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.159881 restraints weight = 1951.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.160950 restraints weight = 1441.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7176
moved from start:          0.2755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2673  Z= 0.129
  Angle     :  0.672   9.651   3627  Z= 0.322
  Chirality :  0.041   0.126    437
  Planarity :  0.006   0.057    441
  Dihedral  :  4.869  44.686    367
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  6.81 %
    Allowed  : 25.09 %
    Favored  : 68.10 %
  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:  1.68 (0.47), residues: 336
  helix:  1.64 (0.33), residues: 267
  sheet:  None (None), residues: 0
  loop : -0.87 (0.71), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 188 
 TYR   0.007   0.001   TYR A 421 
 PHE   0.016   0.001   PHE A 237 
 TRP   0.003   0.001   TRP A 450 
 HIS   0.002   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 2673)
  covalent geometry    : angle       0.67184 ( 3627)
  hydrogen bonds       : bond        0.03698 (  196)
  hydrogen bonds       : angle       4.06136 (  573)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 MET cc_start: 0.8925 (mtp) cc_final: 0.8707 (mmp)
REVERT: A  340 TYR cc_start: 0.7948 (t80) cc_final: 0.7694 (t80)
REVERT: A  357 TRP cc_start: 0.7085 (OUTLIER) cc_final: 0.6628 (m-10)
  outliers start: 19
  outliers final: 18
  residues processed: 99
  average time/residue: 0.0428
  time to fit residues: 5.4427
Evaluate side-chains
  106 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  333 PHE
Chi-restraints excluded: chain A residue  357 TRP
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  388 PHE
Chi-restraints excluded: chain A residue  465 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 31 optimal weight:    0.1980
   chunk 7 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 22 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4063 r_free = 0.4063 target = 0.166053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.151279 restraints weight = 6828.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.154864 restraints weight = 4078.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.157297 restraints weight = 2692.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.159032 restraints weight = 1892.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.160159 restraints weight = 1396.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2673  Z= 0.132
  Angle     :  0.685  10.390   3627  Z= 0.329
  Chirality :  0.042   0.129    437
  Planarity :  0.006   0.058    441
  Dihedral  :  4.853  44.769    367
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  7.53 %
    Allowed  : 23.66 %
    Favored  : 68.82 %
  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:  1.72 (0.47), residues: 336
  helix:  1.67 (0.32), residues: 267
  sheet:  None (None), residues: 0
  loop : -0.88 (0.72), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 188 
 TYR   0.007   0.001   TYR A 421 
 PHE   0.015   0.001   PHE A 237 
 TRP   0.004   0.001   TRP A 450 
 HIS   0.002   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 2673)
  covalent geometry    : angle       0.68452 ( 3627)
  hydrogen bonds       : bond        0.03661 (  196)
  hydrogen bonds       : angle       4.11743 (  573)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 MET cc_start: 0.8965 (mtp) cc_final: 0.8546 (mmt)
REVERT: A  357 TRP cc_start: 0.7093 (OUTLIER) cc_final: 0.6608 (m-10)
REVERT: A  428 PHE cc_start: 0.8314 (t80) cc_final: 0.8021 (t80)
  outliers start: 21
  outliers final: 20
  residues processed: 98
  average time/residue: 0.0447
  time to fit residues: 5.5222
Evaluate side-chains
  105 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 84
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  333 PHE
Chi-restraints excluded: chain A residue  357 TRP
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  388 PHE
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  465 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 26 optimal weight:    0.0000
   chunk 5 optimal weight:    4.9990
   chunk 15 optimal weight:    0.0060
   chunk 7 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 4 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 17 optimal weight:    0.2980
   chunk 12 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.3400

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.167272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.152366 restraints weight = 6920.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.156109 restraints weight = 4130.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.158586 restraints weight = 2684.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.160262 restraints weight = 1880.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.161495 restraints weight = 1390.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7136
moved from start:          0.2929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2673  Z= 0.130
  Angle     :  0.695  10.876   3627  Z= 0.333
  Chirality :  0.042   0.124    437
  Planarity :  0.006   0.057    441
  Dihedral  :  4.787  43.679    367
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 26.16 %
    Favored  : 67.74 %
  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:  1.63 (0.47), residues: 336
  helix:  1.56 (0.32), residues: 267
  sheet:  None (None), residues: 0
  loop : -0.72 (0.74), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 378 
 TYR   0.009   0.001   TYR A 340 
 PHE   0.015   0.001   PHE A 237 
 TRP   0.002   0.000   TRP A 450 
 HIS   0.002   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 2673)
  covalent geometry    : angle       0.69543 ( 3627)
  hydrogen bonds       : bond        0.03617 (  196)
  hydrogen bonds       : angle       4.13248 (  573)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 MET cc_start: 0.8941 (mtp) cc_final: 0.8525 (mmt)
REVERT: A  357 TRP cc_start: 0.7070 (OUTLIER) cc_final: 0.6587 (m-10)
REVERT: A  428 PHE cc_start: 0.8265 (t80) cc_final: 0.7986 (t80)
  outliers start: 17
  outliers final: 16
  residues processed: 95
  average time/residue: 0.0435
  time to fit residues: 5.2908
Evaluate side-chains
  105 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  333 PHE
Chi-restraints excluded: chain A residue  357 TRP
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  465 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 15 optimal weight:    0.2980
   chunk 23 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.165091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.150697 restraints weight = 6740.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.153865 restraints weight = 4039.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.156499 restraints weight = 2735.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.158209 restraints weight = 1900.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.159494 restraints weight = 1397.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7169
moved from start:          0.2926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2673  Z= 0.138
  Angle     :  0.708  10.533   3627  Z= 0.341
  Chirality :  0.042   0.134    437
  Planarity :  0.006   0.058    441
  Dihedral  :  4.871  44.831    367
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  7.17 %
    Allowed  : 25.45 %
    Favored  : 67.38 %
  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:  1.49 (0.46), residues: 336
  helix:  1.48 (0.32), residues: 267
  sheet:  None (None), residues: 0
  loop : -0.84 (0.74), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 188 
 TYR   0.012   0.001   TYR A 340 
 PHE   0.014   0.001   PHE A 237 
 TRP   0.004   0.001   TRP A 450 
 HIS   0.002   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 2673)
  covalent geometry    : angle       0.70817 ( 3627)
  hydrogen bonds       : bond        0.03775 (  196)
  hydrogen bonds       : angle       4.20235 (  573)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 MET cc_start: 0.8949 (mtp) cc_final: 0.8711 (mmt)
  outliers start: 20
  outliers final: 18
  residues processed: 97
  average time/residue: 0.0457
  time to fit residues: 5.6331
Evaluate side-chains
  105 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  333 PHE
Chi-restraints excluded: chain A residue  357 TRP
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  465 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 3 optimal weight:    7.9990
   chunk 10 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.164441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.150503 restraints weight = 7003.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.153842 restraints weight = 4216.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.156107 restraints weight = 2809.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.157621 restraints weight = 2000.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.158801 restraints weight = 1510.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7207
moved from start:          0.3018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2673  Z= 0.144
  Angle     :  0.735  10.354   3627  Z= 0.353
  Chirality :  0.043   0.131    437
  Planarity :  0.006   0.056    441
  Dihedral  :  5.004  45.412    367
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  6.45 %
    Allowed  : 25.81 %
    Favored  : 67.74 %
  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:  1.44 (0.46), residues: 336
  helix:  1.44 (0.32), residues: 268
  sheet:  None (None), residues: 0
  loop : -0.83 (0.76), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 188 
 TYR   0.013   0.001   TYR A 340 
 PHE   0.014   0.001   PHE A 237 
 TRP   0.004   0.001   TRP A 450 
 HIS   0.002   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 2673)
  covalent geometry    : angle       0.73467 ( 3627)
  hydrogen bonds       : bond        0.03980 (  196)
  hydrogen bonds       : angle       4.25353 (  573)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 659.10 seconds
wall clock time: 12 minutes 4.63 seconds (724.63 seconds total)