Starting phenix.real_space_refine
on Wed Jul 23 09:08:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xiu_38390/07_2025/8xiu_38390.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xiu_38390/07_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_38390/07_2025/8xiu_38390.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xiu_38390/07_2025/8xiu_38390.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xiu_38390/07_2025/8xiu_38390.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xiu_38390/07_2025/8xiu_38390.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 2.53, per 1000 atoms: 0.97
  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: 0.63
  Conformation dependent library (CDL) restraints added in 336.1 milliseconds
  

  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: 0.24
  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: 0.70

  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:
        1.23 -     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:             2.220
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     11.590
  Find NCS groups from input model:        0.030
  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:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.990
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.003   0.001   TRP A 317 
 HIS   0.001   0.000   HIS A 413 
 PHE   0.010   0.001   PHE A 134 
 TYR   0.007   0.001   TYR A 340 
 ARG   0.001   0.000   ARG A  19 

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

*********************** 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  : 0.287 
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: 0.1264
  time to fit residues: 15.9094
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  : 0.294 
-------------------------------------------------------------------------------
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 28 optimal weight:    1.9990
   chunk 25 optimal weight:    0.3980
   chunk 14 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 26 optimal weight:    0.1980
   chunk 10 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4069 r_free = 0.4069 target = 0.165154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.151123 restraints weight = 6807.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.154437 restraints weight = 4119.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.156990 restraints weight = 2788.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7179
moved from start:          0.1497

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= 0.134
  Angle     :  0.656   9.450   3627  Z= 0.309
  Chirality :  0.042   0.139    437
  Planarity :  0.006   0.055    441
  Dihedral  :  5.364  52.942    369
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 20.79 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.48), residues: 336
  helix:  2.04 (0.32), residues: 276
  sheet:  None (None), residues: 0
  loop : -0.71 (0.82), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 450 
 HIS   0.007   0.002   HIS A 352 
 PHE   0.024   0.001   PHE A 237 
 TYR   0.012   0.001   TYR A 421 
 ARG   0.001   0.000   ARG A 378 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03593 (  196)
  hydrogen bonds       : angle       3.83361 (  573)
  covalent geometry    : bond        0.00292 ( 2673)
  covalent geometry    : angle       0.65599 ( 3627)

*********************** 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
  103 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A  157 TYR cc_start: 0.6910 (OUTLIER) cc_final: 0.6549 (m-80)
REVERT: A  229 MET cc_start: 0.8969 (mtp) cc_final: 0.8612 (mmt)
REVERT: A  364 MET cc_start: 0.7557 (mtp) cc_final: 0.7270 (mtm)
REVERT: A  428 PHE cc_start: 0.8156 (t80) cc_final: 0.7630 (t80)
  outliers start: 12
  outliers final: 8
  residues processed: 95
  average time/residue: 0.1001
  time to fit residues: 11.8971
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  : 0.266 
-------------------------------------------------------------------------------
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 20 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.4018 r_free = 0.4018 target = 0.161713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.147792 restraints weight = 6583.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.151112 restraints weight = 3961.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.153468 restraints weight = 2633.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7238
moved from start:          0.2058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2673  Z= 0.150
  Angle     :  0.663   8.580   3627  Z= 0.319
  Chirality :  0.042   0.123    437
  Planarity :  0.006   0.057    441
  Dihedral  :  5.571  52.044    369
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 23.30 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.47), residues: 336
  helix:  1.75 (0.32), residues: 271
  sheet:  None (None), residues: 0
  loop : -0.40 (0.77), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 357 
 HIS   0.005   0.002   HIS A 352 
 PHE   0.021   0.001   PHE A 237 
 TYR   0.011   0.001   TYR A 421 
 ARG   0.002   0.000   ARG A 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03981 (  196)
  hydrogen bonds       : angle       4.03866 (  573)
  covalent geometry    : bond        0.00339 ( 2673)
  covalent geometry    : angle       0.66310 ( 3627)

*********************** 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
  104 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A   35 MET cc_start: 0.7231 (tmm) cc_final: 0.7030 (tmm)
REVERT: A  157 TYR cc_start: 0.6933 (OUTLIER) cc_final: 0.6538 (m-80)
REVERT: A  229 MET cc_start: 0.9011 (mtp) cc_final: 0.8597 (mmt)
REVERT: A  304 ASN cc_start: 0.8705 (m-40) cc_final: 0.8485 (m110)
REVERT: A  396 MET cc_start: 0.7415 (tpt) cc_final: 0.7034 (tpt)
  outliers start: 12
  outliers final: 10
  residues processed: 96
  average time/residue: 0.1104
  time to fit residues: 13.0948
Evaluate side-chains
  100 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
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 31 optimal weight:    1.9990
   chunk 21 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 26 optimal weight:    8.9990
   chunk 29 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0980
   chunk 25 optimal weight:    3.9990
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.164558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.150557 restraints weight = 6422.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.154144 restraints weight = 3810.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.156420 restraints weight = 2467.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.2256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2673  Z= 0.131
  Angle     :  0.650   9.615   3627  Z= 0.312
  Chirality :  0.042   0.119    437
  Planarity :  0.006   0.057    441
  Dihedral  :  5.517  49.923    369
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 24.01 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.46), residues: 336
  helix:  1.71 (0.32), residues: 269
  sheet:  None (None), residues: 0
  loop : -0.78 (0.72), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 450 
 HIS   0.004   0.001   HIS A 352 
 PHE   0.021   0.001   PHE A 392 
 TYR   0.012   0.001   TYR A  47 
 ARG   0.002   0.000   ARG A 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03782 (  196)
  hydrogen bonds       : angle       4.01166 (  573)
  covalent geometry    : bond        0.00290 ( 2673)
  covalent geometry    : angle       0.64990 ( 3627)

*********************** 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
  107 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A   35 MET cc_start: 0.7238 (tmm) cc_final: 0.6968 (tmm)
REVERT: A  157 TYR cc_start: 0.6910 (OUTLIER) cc_final: 0.6658 (m-80)
REVERT: A  229 MET cc_start: 0.8935 (mtp) cc_final: 0.8721 (mmt)
REVERT: A  319 MET cc_start: 0.7502 (tpp) cc_final: 0.7137 (ttt)
REVERT: A  396 MET cc_start: 0.7349 (tpt) cc_final: 0.7001 (tpt)
  outliers start: 16
  outliers final: 13
  residues processed: 99
  average time/residue: 0.1111
  time to fit residues: 13.5119
Evaluate side-chains
  103 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
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  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  388 PHE
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 5 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 14 optimal weight:    0.1980
   chunk 30 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4028 r_free = 0.4028 target = 0.162491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.148244 restraints weight = 6510.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.151854 restraints weight = 3861.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.154216 restraints weight = 2529.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7225
moved from start:          0.2437

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= 0.128
  Angle     :  0.648   8.881   3627  Z= 0.311
  Chirality :  0.041   0.115    437
  Planarity :  0.006   0.057    441
  Dihedral  :  5.483  48.512    369
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  6.81 %
    Allowed  : 24.37 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.46), residues: 336
  helix:  1.74 (0.32), residues: 267
  sheet:  None (None), residues: 0
  loop : -0.78 (0.70), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 450 
 HIS   0.003   0.001   HIS A 352 
 PHE   0.020   0.001   PHE A 392 
 TYR   0.011   0.001   TYR A 340 
 ARG   0.003   0.000   ARG A 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03761 (  196)
  hydrogen bonds       : angle       4.02109 (  573)
  covalent geometry    : bond        0.00280 ( 2673)
  covalent geometry    : angle       0.64816 ( 3627)

*********************** 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
  112 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A   35 MET cc_start: 0.7234 (tmm) cc_final: 0.6929 (tmm)
REVERT: A  157 TYR cc_start: 0.6921 (OUTLIER) cc_final: 0.6703 (m-80)
REVERT: A  229 MET cc_start: 0.8946 (mtp) cc_final: 0.8529 (mmt)
  outliers start: 19
  outliers final: 16
  residues processed: 102
  average time/residue: 0.1007
  time to fit residues: 12.9401
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  : 0.272 
-------------------------------------------------------------------------------
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  157 TYR
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  333 PHE
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  388 PHE
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 29 optimal weight:    0.6980
   chunk 26 optimal weight:    0.1980
   chunk 5 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4046 r_free = 0.4046 target = 0.164258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.150063 restraints weight = 6598.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.153707 restraints weight = 3903.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.156077 restraints weight = 2530.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7207
moved from start:          0.2555

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= 0.128
  Angle     :  0.666  10.289   3627  Z= 0.318
  Chirality :  0.042   0.124    437
  Planarity :  0.006   0.057    441
  Dihedral  :  5.470  47.738    369
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 26.16 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.47), residues: 336
  helix:  1.66 (0.33), residues: 267
  sheet:  None (None), residues: 0
  loop : -0.86 (0.70), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 450 
 HIS   0.003   0.001   HIS A 352 
 PHE   0.017   0.001   PHE A 237 
 TYR   0.011   0.001   TYR A 340 
 ARG   0.004   0.000   ARG A 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03805 (  196)
  hydrogen bonds       : angle       4.08540 (  573)
  covalent geometry    : bond        0.00278 ( 2673)
  covalent geometry    : angle       0.66607 ( 3627)

*********************** 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
  108 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A   35 MET cc_start: 0.7121 (tmm) cc_final: 0.6806 (tmm)
REVERT: A  157 TYR cc_start: 0.6947 (OUTLIER) cc_final: 0.6677 (m-80)
REVERT: A  191 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8639 (tm-30)
REVERT: A  229 MET cc_start: 0.8971 (mtp) cc_final: 0.8511 (mmt)
REVERT: A  243 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7497 (tm-30)
  outliers start: 16
  outliers final: 15
  residues processed: 99
  average time/residue: 0.1154
  time to fit residues: 14.2570
Evaluate side-chains
  104 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
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  157 TYR
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  333 PHE
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 9 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4032 r_free = 0.4032 target = 0.163634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.149166 restraints weight = 6806.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.152827 restraints weight = 4062.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.155342 restraints weight = 2667.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start:          0.2663

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= 0.136
  Angle     :  0.681   9.942   3627  Z= 0.329
  Chirality :  0.042   0.116    437
  Planarity :  0.006   0.058    441
  Dihedral  :  5.526  47.432    369
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  6.45 %
    Allowed  : 26.16 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.47), residues: 336
  helix:  1.62 (0.33), residues: 267
  sheet:  None (None), residues: 0
  loop : -0.83 (0.73), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 450 
 HIS   0.002   0.001   HIS A 352 
 PHE   0.016   0.001   PHE A 237 
 TYR   0.012   0.001   TYR A 340 
 ARG   0.004   0.000   ARG A 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03862 (  196)
  hydrogen bonds       : angle       4.15258 (  573)
  covalent geometry    : bond        0.00302 ( 2673)
  covalent geometry    : angle       0.68104 ( 3627)

*********************** 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: 18
    poor density    : 91
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.7207 (tmm) cc_final: 0.6871 (tmm)
REVERT: A  157 TYR cc_start: 0.6961 (OUTLIER) cc_final: 0.6684 (m-80)
REVERT: A  191 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8798 (tm-30)
REVERT: A  229 MET cc_start: 0.8998 (mtp) cc_final: 0.8515 (mmt)
REVERT: A  243 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7525 (tm-30)
REVERT: A  318 MET cc_start: 0.6896 (ttp) cc_final: 0.6445 (ptm)
  outliers start: 18
  outliers final: 15
  residues processed: 99
  average time/residue: 0.1094
  time to fit residues: 13.5817
Evaluate side-chains
  105 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
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  157 TYR
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  333 PHE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0020
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.6590

-------------------------------------------------------------------------------
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 = 0.4048 r_free = 0.4048 target = 0.164408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.150129 restraints weight = 6889.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.153683 restraints weight = 4128.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.156008 restraints weight = 2675.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.2709

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= 0.130
  Angle     :  0.683  10.162   3627  Z= 0.326
  Chirality :  0.042   0.116    437
  Planarity :  0.006   0.058    441
  Dihedral  :  5.493  46.471    369
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 25.09 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.47), residues: 336
  helix:  1.61 (0.33), residues: 267
  sheet:  None (None), residues: 0
  loop : -0.95 (0.72), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 450 
 HIS   0.002   0.001   HIS A 352 
 PHE   0.016   0.001   PHE A 237 
 TYR   0.011   0.001   TYR A 340 
 ARG   0.003   0.000   ARG A 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03748 (  196)
  hydrogen bonds       : angle       4.15400 (  573)
  covalent geometry    : bond        0.00289 ( 2673)
  covalent geometry    : angle       0.68314 ( 3627)

*********************** 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
  108 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.7118 (tmm) cc_final: 0.6804 (tmm)
REVERT: A  157 TYR cc_start: 0.7022 (OUTLIER) cc_final: 0.6787 (m-80)
REVERT: A  191 GLN cc_start: 0.8953 (tm-30) cc_final: 0.8734 (tm-30)
REVERT: A  229 MET cc_start: 0.9019 (mtp) cc_final: 0.8698 (mmt)
REVERT: A  318 MET cc_start: 0.6817 (ttp) cc_final: 0.6395 (ptm)
  outliers start: 17
  outliers final: 15
  residues processed: 98
  average time/residue: 0.1098
  time to fit residues: 13.2364
Evaluate side-chains
  104 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
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  157 TYR
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  380 ILE
Chi-restraints excluded: chain A residue  384 ILE
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 5 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0570
   chunk 31 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0170
   overall best weight:    0.3936

-------------------------------------------------------------------------------
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 = 0.4057 r_free = 0.4057 target = 0.165407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.150621 restraints weight = 6730.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.154267 restraints weight = 3993.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.156697 restraints weight = 2623.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.2804

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= 0.126
  Angle     :  0.688  11.121   3627  Z= 0.322
  Chirality :  0.041   0.120    437
  Planarity :  0.006   0.054    441
  Dihedral  :  5.352  44.621    369
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 25.45 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.47), residues: 336
  helix:  1.60 (0.33), residues: 267
  sheet:  None (None), residues: 0
  loop : -0.90 (0.72), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 317 
 HIS   0.002   0.001   HIS A 352 
 PHE   0.016   0.001   PHE A 237 
 TYR   0.010   0.001   TYR A 340 
 ARG   0.003   0.000   ARG A 378 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03552 (  196)
  hydrogen bonds       : angle       4.11528 (  573)
  covalent geometry    : bond        0.00273 ( 2673)
  covalent geometry    : angle       0.68798 ( 3627)

*********************** 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: 16
    poor density    : 89
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.7011 (tmm) cc_final: 0.6687 (tmm)
REVERT: A  191 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8703 (tm-30)
REVERT: A  229 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8540 (mmt)
REVERT: A  318 MET cc_start: 0.6830 (ttp) cc_final: 0.6390 (ptm)
REVERT: A  357 TRP cc_start: 0.6901 (m-10) cc_final: 0.6501 (m-10)
  outliers start: 16
  outliers final: 14
  residues processed: 96
  average time/residue: 0.0993
  time to fit residues: 11.8191
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  : 0.287 
-------------------------------------------------------------------------------
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  229 MET
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  333 PHE
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 7 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 18 optimal weight:    0.3980
   chunk 30 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 14 optimal weight:    0.3980
   chunk 4 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0000
   chunk 6 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.4584

-------------------------------------------------------------------------------
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 = 0.4073 r_free = 0.4073 target = 0.166150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.151228 restraints weight = 6632.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.154889 restraints weight = 3969.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.157134 restraints weight = 2613.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7172
moved from start:          0.2919

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     :  0.730  14.765   3627  Z= 0.339
  Chirality :  0.043   0.137    437
  Planarity :  0.006   0.053    441
  Dihedral  :  4.788  44.148    367
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 26.52 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.47), residues: 336
  helix:  1.59 (0.33), residues: 267
  sheet:  None (None), residues: 0
  loop : -0.81 (0.74), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 450 
 HIS   0.002   0.001   HIS A 352 
 PHE   0.016   0.001   PHE A 237 
 TYR   0.010   0.001   TYR A 340 
 ARG   0.006   0.001   ARG A 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03592 (  196)
  hydrogen bonds       : angle       4.17860 (  573)
  covalent geometry    : bond        0.00291 ( 2673)
  covalent geometry    : angle       0.72951 ( 3627)

********************** 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
  104 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.7017 (tmm) cc_final: 0.6701 (tmm)
REVERT: A  229 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8507 (mmt)
  outliers start: 16
  outliers final: 14
  residues processed: 95
  average time/residue: 0.1274
  time to fit residues: 14.7541
Evaluate side-chains
  101 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
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  229 MET
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  333 PHE
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 30 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 3 optimal weight:    6.9990
   chunk 33 optimal weight:    0.2980
   chunk 31 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.165651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.151369 restraints weight = 7001.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.154828 restraints weight = 4225.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.157115 restraints weight = 2790.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7215
moved from start:          0.2983

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= 0.137
  Angle     :  0.746  14.187   3627  Z= 0.346
  Chirality :  0.042   0.118    437
  Planarity :  0.006   0.055    441
  Dihedral  :  4.889  45.044    367
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 26.88 %
    Favored  : 67.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.47), residues: 336
  helix:  1.54 (0.32), residues: 267
  sheet:  None (None), residues: 0
  loop : -0.68 (0.76), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 450 
 HIS   0.002   0.001   HIS A 352 
 PHE   0.015   0.001   PHE A 237 
 TYR   0.010   0.001   TYR A 340 
 ARG   0.004   0.001   ARG A 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03790 (  196)
  hydrogen bonds       : angle       4.22668 (  573)
  covalent geometry    : bond        0.00311 ( 2673)
  covalent geometry    : angle       0.74583 ( 3627)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1299.33 seconds
wall clock time: 23 minutes 23.79 seconds (1403.79 seconds total)