Starting phenix.real_space_refine
on Tue Mar  3 12:13:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8org_17123/03_2026/8org_17123.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8org_17123/03_2026/8org_17123.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8org_17123/03_2026/8org_17123.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8org_17123/03_2026/8org_17123.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8org_17123/03_2026/8org_17123.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8org_17123/03_2026/8org_17123.map"
  }
  resolution = 2.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    1206      2.51       5
     N     357      2.21       5
     O     372      1.98       5
     H    2025      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3966
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 1322
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 1322
          Classifications: {'peptide': 86}
          Link IDs: {'PTRANS': 3, 'TRANS': 82}
  Restraints were copied for chains:
    A, C
  Time building chain proxies: 0.77, per 1000 atoms: 0.19
  Number of scatterers: 3966
  At special positions: 0
  Unit cell: (70.8825, 92.6925, 35.9865, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       6     16.00
     O     372      8.00
     N     357      7.00
     C    1206      6.00
     H    2025      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.33
  Conformation dependent library (CDL) restraints added in 90.6 milliseconds
  

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  456

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 11 sheets defined
      0.0% alpha, 45.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 278 through 283
      removed outlier: 6.401A  pdb=" N   ILE B 278 " --> pdb=" O   ASN C 279 " (cutoff:3.500A)
      removed outlier: 8.115A  pdb=" N   LYS C 281 " --> pdb=" O   ILE B 278 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   LYS B 280 " --> pdb=" O   LYS C 281 " (cutoff:3.500A)
      removed outlier: 7.826A  pdb=" N   ASP C 283 " --> pdb=" O   LYS B 280 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   LEU B 282 " --> pdb=" O   ASP C 283 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 286 through 289
    Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 299
      removed outlier: 6.398A  pdb=" N   ILE B 297 " --> pdb=" O   LYS C 298 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 310
      removed outlier: 6.827A  pdb=" N   GLY B 304 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
      removed outlier: 5.946A  pdb=" N   GLY B 303 " --> pdb=" O   GLY C 304 " (cutoff:3.500A)
      removed outlier: 8.387A  pdb=" N   VAL C 306 " --> pdb=" O   GLY B 303 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   SER B 305 " --> pdb=" O   VAL C 306 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   ILE C 308 " --> pdb=" O   SER B 305 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   GLN B 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 7.626A  pdb=" N   TYR C 310 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   VAL B 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 318
      removed outlier: 6.459A  pdb=" N   ASP B 314 " --> pdb=" O   LEU A 315 " (cutoff:3.500A)
      removed outlier: 7.889A  pdb=" N   LYS A 317 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   SER B 316 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   VAL B 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   SER C 316 " --> pdb=" O   VAL B 313 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   LEU B 315 " --> pdb=" O   SER C 316 " (cutoff:3.500A)
      removed outlier: 7.813A  pdb=" N   VAL C 318 " --> pdb=" O   LEU B 315 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   LYS B 317 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 321 through 322
      removed outlier: 6.760A  pdb=" N   LYS B 321 " --> pdb=" O   CYS C 322 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 327 through 330
      removed outlier: 6.457A  pdb=" N   ASN B 327 " --> pdb=" O   ILE C 328 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   HIS C 330 " --> pdb=" O   ASN B 327 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   HIS B 329 " --> pdb=" O   HIS C 330 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 336 through 341
      removed outlier: 6.392A  pdb=" N   VAL B 337 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   LYS A 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   VAL B 339 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 344 through 346
    Processing sheet with id=AB1, first strand: chain 'A' and resid 350 through 354
    Processing sheet with id=AB2, first strand: chain 'A' and resid 360 through 361
      removed outlier: 6.729A  pdb=" N   ILE B 360 " --> pdb=" O   THR A 361 " (cutoff:3.500A)

    42 hydrogen bonds defined for protein.
    126 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: 0.72

  Time building geometry restraints manager: 0.46 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 2019
        1.03 -     1.22: 6
        1.22 -     1.41: 755
        1.41 -     1.61: 1204
        1.61 -     1.80: 6
  Bond restraints: 3990
  Sorted by residual:
  bond pdb=" CB  PRO C 312 "
       pdb=" CG  PRO C 312 "
    ideal  model  delta    sigma   weight residual
    1.492  1.411  0.081 5.00e-02 4.00e+02 2.62e+00
  bond pdb=" CB  PRO B 312 "
       pdb=" CG  PRO B 312 "
    ideal  model  delta    sigma   weight residual
    1.492  1.411  0.081 5.00e-02 4.00e+02 2.59e+00
  bond pdb=" CB  PRO A 312 "
       pdb=" CG  PRO A 312 "
    ideal  model  delta    sigma   weight residual
    1.492  1.412  0.080 5.00e-02 4.00e+02 2.56e+00
  bond pdb=" CE  LYS C 311 "
       pdb=" NZ  LYS C 311 "
    ideal  model  delta    sigma   weight residual
    1.489  1.442  0.047 3.00e-02 1.11e+03 2.41e+00
  bond pdb=" CE  LYS A 311 "
       pdb=" NZ  LYS A 311 "
    ideal  model  delta    sigma   weight residual
    1.489  1.443  0.046 3.00e-02 1.11e+03 2.40e+00
  ... (remaining 3985 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 6364
        1.52 -     3.05: 757
        3.05 -     4.57: 126
        4.57 -     6.10: 25
        6.10 -     7.62: 9
  Bond angle restraints: 7281
  Sorted by residual:
  angle pdb=" CA  LYS C 281 "
        pdb=" CB  LYS C 281 "
        pdb=" CG  LYS C 281 "
      ideal   model   delta    sigma   weight residual
     114.10  120.92   -6.82 2.00e+00 2.50e-01 1.16e+01
  angle pdb=" CA  LYS A 281 "
        pdb=" CB  LYS A 281 "
        pdb=" CG  LYS A 281 "
      ideal   model   delta    sigma   weight residual
     114.10  120.89   -6.79 2.00e+00 2.50e-01 1.15e+01
  angle pdb=" CA  LYS B 281 "
        pdb=" CB  LYS B 281 "
        pdb=" CG  LYS B 281 "
      ideal   model   delta    sigma   weight residual
     114.10  120.87   -6.77 2.00e+00 2.50e-01 1.15e+01
  angle pdb=" N   LYS A 281 "
        pdb=" CA  LYS A 281 "
        pdb=" C   LYS A 281 "
      ideal   model   delta    sigma   weight residual
     109.23  114.31   -5.08 1.55e+00 4.16e-01 1.08e+01
  angle pdb=" N   LYS B 281 "
        pdb=" CA  LYS B 281 "
        pdb=" C   LYS B 281 "
      ideal   model   delta    sigma   weight residual
     109.23  114.30   -5.07 1.55e+00 4.16e-01 1.07e+01
  ... (remaining 7276 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.45: 1566
       13.45 -    26.91: 149
       26.91 -    40.36: 31
       40.36 -    53.81: 36
       53.81 -    67.26: 54
  Dihedral angle restraints: 1836
    sinusoidal: 1059
      harmonic: 777
  Sorted by residual:
  dihedral pdb=" CA  LEU A 357 "
           pdb=" C   LEU A 357 "
           pdb=" N   ASP A 358 "
           pdb=" CA  ASP A 358 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.58   24.42     0      5.00e+00 4.00e-02 2.39e+01
  dihedral pdb=" CA  LEU B 357 "
           pdb=" C   LEU B 357 "
           pdb=" N   ASP B 358 "
           pdb=" CA  ASP B 358 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.60   24.40     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" CA  LEU C 357 "
           pdb=" C   LEU C 357 "
           pdb=" N   ASP C 358 "
           pdb=" CA  ASP C 358 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.62   24.38     0      5.00e+00 4.00e-02 2.38e+01
  ... (remaining 1833 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.076: 228
       0.076 -    0.152: 63
       0.152 -    0.227: 3
       0.227 -    0.303: 3
       0.303 -    0.378: 3
  Chirality restraints: 300
  Sorted by residual:
  chirality pdb=" CB  ILE B 360 "
            pdb=" CA  ILE B 360 "
            pdb=" CG1 ILE B 360 "
            pdb=" CG2 ILE B 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.38 2.00e-01 2.50e+01 3.57e+00
  chirality pdb=" CB  ILE C 360 "
            pdb=" CA  ILE C 360 "
            pdb=" CG1 ILE C 360 "
            pdb=" CG2 ILE C 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.38 2.00e-01 2.50e+01 3.57e+00
  chirality pdb=" CB  ILE A 360 "
            pdb=" CA  ILE A 360 "
            pdb=" CG1 ILE A 360 "
            pdb=" CG2 ILE A 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.38 2.00e-01 2.50e+01 3.54e+00
  ... (remaining 297 not shown)

  Planarity restraints: 582
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 288 "   -0.025 2.00e-02 2.50e+03   3.22e-02 1.55e+01
        pdb=" CD  GLN B 288 "    0.017 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 288 "    0.003 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 288 "    0.053 2.00e-02 2.50e+03
        pdb="HE21 GLN B 288 "    0.001 2.00e-02 2.50e+03
        pdb="HE22 GLN B 288 "   -0.049 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 288 "   -0.025 2.00e-02 2.50e+03   3.21e-02 1.55e+01
        pdb=" CD  GLN A 288 "    0.017 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 288 "    0.003 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 288 "    0.054 2.00e-02 2.50e+03
        pdb="HE21 GLN A 288 "    0.001 2.00e-02 2.50e+03
        pdb="HE22 GLN A 288 "   -0.049 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN C 288 "   -0.025 2.00e-02 2.50e+03   3.20e-02 1.53e+01
        pdb=" CD  GLN C 288 "    0.017 2.00e-02 2.50e+03
        pdb=" OE1 GLN C 288 "    0.003 2.00e-02 2.50e+03
        pdb=" NE2 GLN C 288 "    0.053 2.00e-02 2.50e+03
        pdb="HE21 GLN C 288 "    0.001 2.00e-02 2.50e+03
        pdb="HE22 GLN C 288 "   -0.049 2.00e-02 2.50e+03
  ... (remaining 579 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.32: 1175
        2.32 -     2.89: 9040
        2.89 -     3.46: 8824
        3.46 -     4.03: 13749
        4.03 -     4.60: 19241
  Nonbonded interactions: 52029
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP C 295 "
            pdb=" HZ3 LYS C 311 "
     model   vdw
     1.746 2.450
  nonbonded pdb=" OD2 ASP B 295 "
            pdb=" HZ3 LYS B 311 "
     model   vdw
     1.747 2.450
  nonbonded pdb=" OD2 ASP A 295 "
            pdb=" HZ3 LYS A 311 "
     model   vdw
     1.748 2.450
  nonbonded pdb="HD22 ASN A 296 "
            pdb=" OD2 ASP A 358 "
     model   vdw
     1.764 2.450
  nonbonded pdb="HD22 ASN B 296 "
            pdb=" OD2 ASP B 358 "
     model   vdw
     1.765 2.450
  ... (remaining 52024 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.310
  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:             0.030
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.750
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
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      :  0.010   0.081   1965  Z= 0.359
  Angle     :  1.263   7.621   2628  Z= 0.667
  Chirality :  0.075   0.378    300
  Planarity :  0.005   0.032    336
  Dihedral  : 11.917  66.727    759
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  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 are not related in a simple way.
  whole: -2.52 (0.43), residues: 252
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.91 (0.33), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG C 349 
 TYR   0.016   0.009   TYR A 310 
 PHE   0.012   0.005   PHE C 346 
 HIS   0.019   0.006   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00961 ( 1965)
  covalent geometry    : angle       1.26255 ( 2628)
  hydrogen bonds       : bond        0.12215 (   42)
  hydrogen bonds       : angle       7.80445 (  126)

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

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

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  281 LYS cc_start: 0.7478 (ptpt) cc_final: 0.7251 (ptmt)
REVERT: B  317 LYS cc_start: 0.8471 (tttt) cc_final: 0.8201 (tttm)
REVERT: B  331 LYS cc_start: 0.8517 (mttt) cc_final: 0.8284 (mttt)
REVERT: B  341 SER cc_start: 0.8619 (m) cc_final: 0.8368 (t)
REVERT: A  281 LYS cc_start: 0.8333 (ptpt) cc_final: 0.8063 (ptmt)
REVERT: A  340 LYS cc_start: 0.8368 (mttt) cc_final: 0.8123 (mtpp)
REVERT: A  349 ARG cc_start: 0.7519 (mtt180) cc_final: 0.6035 (mmp-170)
REVERT: A  351 GLN cc_start: 0.7767 (tt0) cc_final: 0.7489 (tt0)
REVERT: A  356 SER cc_start: 0.8520 (t) cc_final: 0.8006 (p)
REVERT: A  358 ASP cc_start: 0.7114 (t0) cc_final: 0.6880 (t0)
REVERT: C  314 ASP cc_start: 0.7593 (t0) cc_final: 0.7113 (t0)
REVERT: C  331 LYS cc_start: 0.8541 (mttt) cc_final: 0.8314 (mttt)
REVERT: C  338 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7337 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 1.2889
  time to fit residues: 125.4764
Evaluate side-chains
  58 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 286 ASN
A 336 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.149914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.130849 restraints weight = 6829.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.4140 rms_B_bonded: 1.97
r_work: 0.4058 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3961 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.4238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   1965  Z= 0.116
  Angle     :  0.577   3.950   2628  Z= 0.294
  Chirality :  0.052   0.141    300
  Planarity :  0.003   0.022    336
  Dihedral  :  6.548  17.678    261
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 0.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 13.60 %
    Favored  : 82.46 %
  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 are not related in a simple way.
  whole: -2.86 (0.40), residues: 252
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.17 (0.31), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 349 
 TYR   0.003   0.001   TYR C 310 
 PHE   0.004   0.001   PHE C 346 
 HIS   0.004   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 1965)
  covalent geometry    : angle       0.57689 ( 2628)
  hydrogen bonds       : bond        0.02354 (   42)
  hydrogen bonds       : angle       6.21031 (  126)

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

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

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  341 SER cc_start: 0.8836 (m) cc_final: 0.8634 (t)
REVERT: B  345 ASP cc_start: 0.8188 (m-30) cc_final: 0.7969 (t70)
REVERT: A  340 LYS cc_start: 0.8688 (mttt) cc_final: 0.8324 (mtpp)
REVERT: A  349 ARG cc_start: 0.7884 (mtt180) cc_final: 0.6548 (mtt-85)
REVERT: C  317 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8828 (tptm)
REVERT: C  338 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7900 (mp0)
REVERT: C  340 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8612 (mtpm)
  outliers start: 9
  outliers final: 1
  residues processed: 71
  average time/residue: 1.0459
  time to fit residues: 75.7018
Evaluate side-chains
  58 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain C residue  317 LYS
Chi-restraints excluded: chain C residue  340 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 18 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
B 279 ASN
B 286 ASN
A 336 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.140526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.121418 restraints weight = 6905.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.4024 rms_B_bonded: 1.92
r_work: 0.3940 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3849 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.5168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   1965  Z= 0.160
  Angle     :  0.549   3.961   2628  Z= 0.282
  Chirality :  0.052   0.127    300
  Planarity :  0.003   0.026    336
  Dihedral  :  6.081  16.786    261
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 1.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 18.42 %
    Favored  : 78.07 %
  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 are not related in a simple way.
  whole: -2.97 (0.41), residues: 252
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.25 (0.31), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.004   0.001   TYR A 310 
 PHE   0.003   0.001   PHE C 346 
 HIS   0.004   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 1965)
  covalent geometry    : angle       0.54900 ( 2628)
  hydrogen bonds       : bond        0.02270 (   42)
  hydrogen bonds       : angle       5.64626 (  126)

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

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

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.078 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8704 (mttt) cc_final: 0.8344 (mtpp)
REVERT: A  349 ARG cc_start: 0.8140 (mtt180) cc_final: 0.6180 (mmp-170)
REVERT: A  351 GLN cc_start: 0.8078 (mt0) cc_final: 0.7873 (mt0)
REVERT: C  338 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7890 (mp0)
REVERT: C  340 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8548 (mtpm)
  outliers start: 8
  outliers final: 4
  residues processed: 61
  average time/residue: 0.7873
  time to fit residues: 49.1936
Evaluate side-chains
  59 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  340 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 4 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 18 optimal weight:    0.3980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
B 279 ASN
A 336 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.144465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.125872 restraints weight = 6749.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.4089 rms_B_bonded: 1.92
r_work: 0.4004 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3912 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.5605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   1965  Z= 0.105
  Angle     :  0.494   3.617   2628  Z= 0.253
  Chirality :  0.052   0.126    300
  Planarity :  0.003   0.026    336
  Dihedral  :  5.428  15.296    261
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 0.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 20.61 %
    Favored  : 77.63 %
  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 are not related in a simple way.
  whole: -3.00 (0.40), residues: 252
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.28 (0.31), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.003   0.001   TYR A 310 
 PHE   0.002   0.001   PHE B 346 
 HIS   0.003   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 1965)
  covalent geometry    : angle       0.49397 ( 2628)
  hydrogen bonds       : bond        0.01862 (   42)
  hydrogen bonds       : angle       5.14004 (  126)

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

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

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.069 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  336 GLN cc_start: 0.8548 (mt0) cc_final: 0.8191 (tt0)
REVERT: A  340 LYS cc_start: 0.8728 (mttt) cc_final: 0.8307 (mtpp)
REVERT: A  349 ARG cc_start: 0.8109 (mtt180) cc_final: 0.6122 (mmp-170)
REVERT: C  338 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7893 (mp0)
  outliers start: 4
  outliers final: 2
  residues processed: 55
  average time/residue: 0.8097
  time to fit residues: 45.5880
Evaluate side-chains
  53 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 51
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  344 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 15 optimal weight:    0.1980
   chunk 12 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
B 279 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.139843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.120810 restraints weight = 6817.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.4030 rms_B_bonded: 1.94
r_work: 0.3945 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3850 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.5704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   1965  Z= 0.135
  Angle     :  0.494   3.540   2628  Z= 0.254
  Chirality :  0.051   0.124    300
  Planarity :  0.003   0.024    336
  Dihedral  :  5.435  15.360    261
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 1.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 18.86 %
    Favored  : 77.19 %
  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 are not related in a simple way.
  whole: -2.91 (0.41), residues: 252
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.21 (0.31), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.004   0.001   TYR A 310 
 PHE   0.003   0.001   PHE A 346 
 HIS   0.002   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 1965)
  covalent geometry    : angle       0.49417 ( 2628)
  hydrogen bonds       : bond        0.01759 (   42)
  hydrogen bonds       : angle       5.04757 (  126)

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

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

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  325 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8692 (mt)
REVERT: A  336 GLN cc_start: 0.8489 (mt0) cc_final: 0.8153 (tt0)
REVERT: A  340 LYS cc_start: 0.8718 (mttt) cc_final: 0.8395 (mtpp)
REVERT: A  349 ARG cc_start: 0.8178 (mtt180) cc_final: 0.6072 (mmp-170)
REVERT: A  351 GLN cc_start: 0.7998 (mt0) cc_final: 0.7731 (mt0)
REVERT: C  338 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7920 (mp0)
REVERT: C  340 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8541 (mtpm)
  outliers start: 9
  outliers final: 2
  residues processed: 58
  average time/residue: 0.8533
  time to fit residues: 50.5602
Evaluate side-chains
  57 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain C residue  340 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 14 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 3 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:
B 279 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.143729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.124951 restraints weight = 6891.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.4080 rms_B_bonded: 1.94
r_work: 0.3998 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3905 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.5877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   1965  Z= 0.094
  Angle     :  0.475   3.434   2628  Z= 0.242
  Chirality :  0.051   0.122    300
  Planarity :  0.003   0.025    336
  Dihedral  :  5.089  14.849    261
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 0.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 19.74 %
    Favored  : 78.51 %
  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 are not related in a simple way.
  whole: -2.93 (0.41), residues: 252
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.22 (0.32), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.002   0.001   TYR C 310 
 PHE   0.002   0.001   PHE A 346 
 HIS   0.002   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 1965)
  covalent geometry    : angle       0.47508 ( 2628)
  hydrogen bonds       : bond        0.01589 (   42)
  hydrogen bonds       : angle       4.77919 (  126)

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

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

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  336 GLN cc_start: 0.8522 (mt0) cc_final: 0.8212 (tt0)
REVERT: A  340 LYS cc_start: 0.8743 (mttt) cc_final: 0.8433 (mtpp)
REVERT: A  349 ARG cc_start: 0.8180 (mtt180) cc_final: 0.6122 (mmp-170)
REVERT: A  351 GLN cc_start: 0.8005 (mt0) cc_final: 0.7739 (mt0)
REVERT: C  338 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7910 (mp0)
  outliers start: 4
  outliers final: 2
  residues processed: 53
  average time/residue: 0.8650
  time to fit residues: 46.9184
Evaluate side-chains
  51 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  344 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
B 336 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.141125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.122326 restraints weight = 6901.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.4045 rms_B_bonded: 1.93
r_work: 0.3960 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3867 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.5924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   1965  Z= 0.120
  Angle     :  0.483   3.606   2628  Z= 0.246
  Chirality :  0.051   0.122    300
  Planarity :  0.003   0.025    336
  Dihedral  :  5.153  15.177    261
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 0.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 19.30 %
    Favored  : 78.07 %
  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 are not related in a simple way.
  whole: -2.88 (0.42), residues: 252
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.18 (0.32), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.003   0.001   TYR A 310 
 PHE   0.003   0.001   PHE A 346 
 HIS   0.001   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 1965)
  covalent geometry    : angle       0.48313 ( 2628)
  hydrogen bonds       : bond        0.01593 (   42)
  hydrogen bonds       : angle       4.77968 (  126)

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

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

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  336 GLN cc_start: 0.8480 (mt0) cc_final: 0.8158 (tt0)
REVERT: A  340 LYS cc_start: 0.8738 (mttt) cc_final: 0.8417 (mtpp)
REVERT: A  349 ARG cc_start: 0.8212 (mtt180) cc_final: 0.6074 (mmp-170)
REVERT: A  351 GLN cc_start: 0.8037 (mt0) cc_final: 0.7771 (mt0)
REVERT: C  338 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7924 (mp0)
  outliers start: 6
  outliers final: 5
  residues processed: 52
  average time/residue: 0.8979
  time to fit residues: 47.6683
Evaluate side-chains
  54 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  344 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0570
   chunk 5 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   overall best weight:    1.1904

-------------------------------------------------------------------------------
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 = 0.4285 r_free = 0.4285 target = 0.141972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.123484 restraints weight = 6864.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.4064 rms_B_bonded: 1.91
r_work: 0.3980 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3887 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.5985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   1965  Z= 0.107
  Angle     :  0.473   3.621   2628  Z= 0.241
  Chirality :  0.051   0.121    300
  Planarity :  0.003   0.025    336
  Dihedral  :  5.037  15.071    261
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 0.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.86 %
    Favored  : 78.51 %
  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 are not related in a simple way.
  whole: -2.93 (0.42), residues: 252
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.22 (0.32), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.003   0.001   TYR A 310 
 PHE   0.002   0.001   PHE C 346 
 HIS   0.001   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 1965)
  covalent geometry    : angle       0.47306 ( 2628)
  hydrogen bonds       : bond        0.01530 (   42)
  hydrogen bonds       : angle       4.69297 (  126)

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

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

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.074 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  284 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8570 (tp)
REVERT: A  325 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8672 (mt)
REVERT: A  336 GLN cc_start: 0.8533 (mt0) cc_final: 0.8209 (tt0)
REVERT: A  340 LYS cc_start: 0.8739 (mttt) cc_final: 0.8421 (mtpp)
REVERT: A  349 ARG cc_start: 0.8212 (mtt180) cc_final: 0.6166 (mmp-170)
REVERT: C  338 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7894 (mp0)
  outliers start: 6
  outliers final: 4
  residues processed: 50
  average time/residue: 0.9126
  time to fit residues: 46.6559
Evaluate side-chains
  53 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  344 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 8 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
B 336 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.140313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.121382 restraints weight = 6873.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.4037 rms_B_bonded: 1.94
r_work: 0.3950 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3857 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.5997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   1965  Z= 0.128
  Angle     :  0.484   3.849   2628  Z= 0.248
  Chirality :  0.051   0.121    300
  Planarity :  0.003   0.025    336
  Dihedral  :  5.144  15.376    261
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 1.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 18.86 %
    Favored  : 78.07 %
  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 are not related in a simple way.
  whole: -2.90 (0.42), residues: 252
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.20 (0.32), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.003   0.001   TYR A 310 
 PHE   0.003   0.001   PHE A 346 
 HIS   0.001   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 1965)
  covalent geometry    : angle       0.48390 ( 2628)
  hydrogen bonds       : bond        0.01622 (   42)
  hydrogen bonds       : angle       4.80499 (  126)

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

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

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  284 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8586 (tp)
REVERT: A  325 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8660 (mt)
REVERT: A  336 GLN cc_start: 0.8478 (mt0) cc_final: 0.8144 (tt0)
REVERT: A  340 LYS cc_start: 0.8749 (mttt) cc_final: 0.8413 (mtpp)
REVERT: A  349 ARG cc_start: 0.8222 (mtt180) cc_final: 0.6193 (mmp-170)
REVERT: C  338 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7926 (mp0)
  outliers start: 7
  outliers final: 5
  residues processed: 51
  average time/residue: 0.9808
  time to fit residues: 51.1055
Evaluate side-chains
  55 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  344 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0170
   chunk 3 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.7220

-------------------------------------------------------------------------------
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 = 0.4317 r_free = 0.4317 target = 0.145162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.126541 restraints weight = 6710.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.4102 rms_B_bonded: 1.94
r_work: 0.4020 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3925 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.6110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   1965  Z= 0.086
  Angle     :  0.465   3.888   2628  Z= 0.236
  Chirality :  0.051   0.124    300
  Planarity :  0.003   0.027    336
  Dihedral  :  4.832  14.734    261
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 1.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 19.74 %
    Favored  : 78.07 %
  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 are not related in a simple way.
  whole: -2.96 (0.41), residues: 252
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.25 (0.31), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.002   0.001   TYR C 310 
 PHE   0.002   0.000   PHE A 346 
 HIS   0.003   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 ( 1965)
  covalent geometry    : angle       0.46478 ( 2628)
  hydrogen bonds       : bond        0.01441 (   42)
  hydrogen bonds       : angle       4.61961 (  126)

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

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

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  284 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8574 (tp)
REVERT: A  336 GLN cc_start: 0.8518 (mt0) cc_final: 0.8206 (tt0)
REVERT: A  340 LYS cc_start: 0.8768 (mttt) cc_final: 0.8454 (mtpp)
REVERT: A  349 ARG cc_start: 0.8223 (mtt180) cc_final: 0.6145 (mmp-170)
REVERT: C  338 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7875 (mp0)
  outliers start: 5
  outliers final: 4
  residues processed: 52
  average time/residue: 1.0011
  time to fit residues: 53.1148
Evaluate side-chains
  54 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  344 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 18 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0040
   overall best weight:    1.1594

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

Flipped N/Q/H residues before XYZ refinement:
B 336 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.142463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.123308 restraints weight = 6748.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.4075 rms_B_bonded: 1.93
r_work: 0.3990 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3897 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.6102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   1965  Z= 0.106
  Angle     :  0.466   3.997   2628  Z= 0.238
  Chirality :  0.051   0.120    300
  Planarity :  0.003   0.026    336
  Dihedral  :  4.906  14.933    261
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 1.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 20.18 %
    Favored  : 77.63 %
  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 are not related in a simple way.
  whole: -2.96 (0.41), residues: 252
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.25 (0.31), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.003   0.001   TYR B 310 
 PHE   0.003   0.001   PHE A 346 
 HIS   0.002   0.000   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 1965)
  covalent geometry    : angle       0.46578 ( 2628)
  hydrogen bonds       : bond        0.01482 (   42)
  hydrogen bonds       : angle       4.39033 (  126)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2515.19 seconds
wall clock time: 43 minutes 10.83 seconds (2590.83 seconds total)