Starting phenix.real_space_refine
on Fri Aug 22 13:19:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qcr_18333/08_2025/8qcr_18333.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qcr_18333/08_2025/8qcr_18333.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qcr_18333/08_2025/8qcr_18333.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qcr_18333/08_2025/8qcr_18333.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qcr_18333/08_2025/8qcr_18333.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qcr_18333/08_2025/8qcr_18333.map"
  }
  resolution = 2.75
  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=   0.001
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       3      5.16       5
     C     966      2.51       5
     N     285      2.21       5
     O     291      1.98       5
     H    1608      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3153
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 1051
          Classifications: {'peptide': 68}
          Link IDs: {'PTRANS': 3, 'TRANS': 64}
    Chain: "C"
      Number of atoms: 1051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 1051
          Classifications: {'peptide': 68}
          Link IDs: {'PTRANS': 3, 'TRANS': 64}
    Chain: "E"
      Number of atoms: 1051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 1051
          Classifications: {'peptide': 68}
          Link IDs: {'PTRANS': 3, 'TRANS': 64}
  Time building chain proxies: 0.60, per 1000 atoms: 0.19
  Number of scatterers: 3153
  At special positions: 0
  Unit cell: (99.704, 70.864, 37.08, 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       3     16.00
     O     291      8.00
     N     285      7.00
     C     966      6.00
     H    1608      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: 0.18
  Conformation dependent library (CDL) restraints added in 84.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  354

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 64.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 309 through 310
      removed outlier: 6.614A  pdb=" N   VAL C 309 " --> pdb=" O   TYR E 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314
      removed outlier: 6.715A  pdb=" N   VAL C 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 325
      removed outlier: 6.754A  pdb=" N   VAL A 318 " --> pdb=" O   THR E 319 " (cutoff:3.500A)
      removed outlier: 8.060A  pdb=" N   LYS E 321 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   SER A 320 " --> pdb=" O   LYS E 321 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   GLY E 323 " --> pdb=" O   SER A 320 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   CYS A 322 " --> pdb=" O   GLY E 323 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   LEU E 325 " --> pdb=" O   CYS A 322 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   SER A 324 " --> pdb=" O   LEU E 325 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330
      removed outlier: 6.313A  pdb=" N   ILE C 328 " --> pdb=" O   HIS E 329 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 337 through 342
      removed outlier: 6.513A  pdb=" N   VAL A 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 7.901A  pdb=" N   LYS E 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   VAL A 339 " --> pdb=" O   LYS E 340 " (cutoff:3.500A)
      removed outlier: 7.883A  pdb=" N   GLU E 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   SER A 341 " --> pdb=" O   GLU E 342 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 346
      removed outlier: 6.529A  pdb=" N   ASP C 345 " --> pdb=" O   PHE E 346 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 350 through 362
      removed outlier: 8.920A  pdb=" N   GLN A 351 " --> pdb=" O   SER E 352 " (cutoff:3.500A)
      removed outlier: 10.505A  pdb=" N   ILE E 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 9.159A  pdb=" N   LYS A 353 " --> pdb=" O   ILE E 354 " (cutoff:3.500A)
      removed outlier: 10.114A  pdb=" N   SER E 356 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   GLY A 355 " --> pdb=" O   SER E 356 " (cutoff:3.500A)
      removed outlier: 8.093A  pdb=" N   ASP E 358 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   LEU A 357 " --> pdb=" O   ASP E 358 " (cutoff:3.500A)
      removed outlier: 7.884A  pdb=" N   ILE E 360 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   ASN A 359 " --> pdb=" O   ILE E 360 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   HIS E 362 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   THR A 361 " --> pdb=" O   HIS E 362 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 350 through 362
      removed outlier: 8.920A  pdb=" N   GLN A 351 " --> pdb=" O   SER E 352 " (cutoff:3.500A)
      removed outlier: 10.505A  pdb=" N   ILE E 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 9.159A  pdb=" N   LYS A 353 " --> pdb=" O   ILE E 354 " (cutoff:3.500A)
      removed outlier: 10.114A  pdb=" N   SER E 356 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   GLY A 355 " --> pdb=" O   SER E 356 " (cutoff:3.500A)
      removed outlier: 8.093A  pdb=" N   ASP E 358 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   LEU A 357 " --> pdb=" O   ASP E 358 " (cutoff:3.500A)
      removed outlier: 7.884A  pdb=" N   ILE E 360 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   ASN A 359 " --> pdb=" O   ILE E 360 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   HIS E 362 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   THR A 361 " --> pdb=" O   HIS E 362 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 368 through 374
      removed outlier: 6.370A  pdb=" N   LYS C 369 " --> pdb=" O   LYS E 370 " (cutoff:3.500A)
      removed outlier: 8.064A  pdb=" N   GLU E 372 " --> pdb=" O   LYS C 369 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   ILE C 371 " --> pdb=" O   GLU E 372 " (cutoff:3.500A)
      removed outlier: 8.101A  pdb=" N   HIS E 374 " --> pdb=" O   ILE C 371 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   THR C 373 " --> pdb=" O   HIS E 374 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 333 through 334
      removed outlier: 6.871A  pdb=" N   GLY C 333 " --> pdb=" O   GLY E 334 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    33 hydrogen bonds defined for protein.
    99 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: 0.49

  Time building geometry restraints manager: 0.27 seconds

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

  Histogram of bond lengths:
        0.95 -     1.12: 1605
        1.12 -     1.29: 261
        1.29 -     1.47: 487
        1.47 -     1.64: 821
        1.64 -     1.81: 3
  Bond restraints: 3177
  Sorted by residual:
  bond pdb=" N   ILE C 308 "
       pdb=" H   ILE C 308 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  bond pdb=" N   SER A 324 "
       pdb=" H   SER A 324 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  bond pdb=" N   GLY C 326 "
       pdb=" H   GLY C 326 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" N   VAL C 309 "
       pdb=" H   VAL C 309 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" ND2 ASN E 359 "
       pdb="HD21 ASN E 359 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
  ... (remaining 3172 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.43: 4867
        2.43 -     4.87: 722
        4.87 -     7.30: 203
        7.30 -     9.74: 7
        9.74 -    12.17: 3
  Bond angle restraints: 5802
  Sorted by residual:
  angle pdb=" CA  ASP E 345 "
        pdb=" CB  ASP E 345 "
        pdb=" CG  ASP E 345 "
      ideal   model   delta    sigma   weight residual
     112.60  118.01   -5.41 1.00e+00 1.00e+00 2.92e+01
  angle pdb=" CA  ASP A 358 "
        pdb=" CB  ASP A 358 "
        pdb=" CG  ASP A 358 "
      ideal   model   delta    sigma   weight residual
     112.60  117.08   -4.48 1.00e+00 1.00e+00 2.01e+01
  angle pdb=" CA  ASP A 345 "
        pdb=" CB  ASP A 345 "
        pdb=" CG  ASP A 345 "
      ideal   model   delta    sigma   weight residual
     112.60  117.06   -4.46 1.00e+00 1.00e+00 1.99e+01
  angle pdb=" CA  GLY E 355 "
        pdb=" C   GLY E 355 "
        pdb=" N   SER E 356 "
      ideal   model   delta    sigma   weight residual
     114.84  119.43   -4.59 1.06e+00 8.90e-01 1.87e+01
  angle pdb=" CB  HIS E 362 "
        pdb=" CG  HIS E 362 "
        pdb=" CD2 HIS E 362 "
      ideal   model   delta    sigma   weight residual
     131.20  125.68    5.52 1.30e+00 5.92e-01 1.80e+01
  ... (remaining 5797 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.36: 1277
       13.36 -    26.71: 88
       26.71 -    40.07: 33
       40.07 -    53.42: 22
       53.42 -    66.78: 41
  Dihedral angle restraints: 1461
    sinusoidal: 840
      harmonic: 621
  Sorted by residual:
  dihedral pdb=" CA  LYS E 321 "
           pdb=" C   LYS E 321 "
           pdb=" N   CYS E 322 "
           pdb=" CA  CYS E 322 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.34  -21.66     0      5.00e+00 4.00e-02 1.88e+01
  dihedral pdb=" CA  VAL C 350 "
           pdb=" C   VAL C 350 "
           pdb=" N   GLN C 351 "
           pdb=" CA  GLN C 351 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.56   20.44     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" CA  VAL E 350 "
           pdb=" C   VAL E 350 "
           pdb=" N   GLN E 351 "
           pdb=" CA  GLN E 351 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.41   18.59     0      5.00e+00 4.00e-02 1.38e+01
  ... (remaining 1458 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 115
       0.052 -    0.104: 77
       0.104 -    0.157: 27
       0.157 -    0.209: 12
       0.209 -    0.261: 3
  Chirality restraints: 234
  Sorted by residual:
  chirality pdb=" CA  LYS C 343 "
            pdb=" N   LYS C 343 "
            pdb=" C   LYS C 343 "
            pdb=" CB  LYS C 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.70e+00
  chirality pdb=" CA  LYS C 347 "
            pdb=" N   LYS C 347 "
            pdb=" C   LYS C 347 "
            pdb=" CB  LYS C 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  VAL E 337 "
            pdb=" N   VAL E 337 "
            pdb=" C   VAL E 337 "
            pdb=" CB  VAL E 337 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.22    0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 231 not shown)

  Planarity restraints: 459
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN E 368 "   -0.090 2.00e-02 2.50e+03   7.98e-02 9.55e+01
        pdb=" CG  ASN E 368 "    0.035 2.00e-02 2.50e+03
        pdb=" OD1 ASN E 368 "    0.054 2.00e-02 2.50e+03
        pdb=" ND2 ASN E 368 "    0.058 2.00e-02 2.50e+03
        pdb="HD21 ASN E 368 "    0.074 2.00e-02 2.50e+03
        pdb="HD22 ASN E 368 "   -0.131 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS E 362 "    0.068 2.00e-02 2.50e+03   3.97e-02 3.55e+01
        pdb=" CG  HIS E 362 "   -0.052 2.00e-02 2.50e+03
        pdb=" ND1 HIS E 362 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD2 HIS E 362 "   -0.041 2.00e-02 2.50e+03
        pdb=" CE1 HIS E 362 "   -0.010 2.00e-02 2.50e+03
        pdb=" NE2 HIS E 362 "   -0.027 2.00e-02 2.50e+03
        pdb=" HD2 HIS E 362 "    0.014 2.00e-02 2.50e+03
        pdb=" HE1 HIS E 362 "    0.041 2.00e-02 2.50e+03
        pdb=" HE2 HIS E 362 "    0.038 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 362 "    0.064 2.00e-02 2.50e+03   3.67e-02 3.03e+01
        pdb=" CG  HIS A 362 "   -0.051 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 362 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 362 "   -0.043 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 362 "   -0.007 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 362 "   -0.020 2.00e-02 2.50e+03
        pdb=" HD2 HIS A 362 "    0.013 2.00e-02 2.50e+03
        pdb=" HE1 HIS A 362 "    0.031 2.00e-02 2.50e+03
        pdb=" HE2 HIS A 362 "    0.038 2.00e-02 2.50e+03
  ... (remaining 456 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 196
        2.16 -     2.77: 5228
        2.77 -     3.38: 8238
        3.38 -     3.99: 10907
        3.99 -     4.60: 15415
  Nonbonded interactions: 39984
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C 314 "
            pdb=" HG  SER C 316 "
     model   vdw
     1.546 2.450
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" HG  SER E 316 "
     model   vdw
     1.575 2.450
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" HG  SER A 316 "
     model   vdw
     1.576 2.450
  nonbonded pdb=" HG  SER A 320 "
            pdb=" O   GLY A 366 "
     model   vdw
     1.644 2.450
  nonbonded pdb=" HG  SER C 320 "
            pdb=" O   GLY C 366 "
     model   vdw
     1.669 2.450
  ... (remaining 39979 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
}

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:             3.090
  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:             0.020
  Extract box with map and model:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.900
  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:5.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
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      :  0.011   0.035   1569  Z= 0.680
  Angle     :  1.777   5.847   2097  Z= 1.194
  Chirality :  0.079   0.261    234
  Planarity :  0.009   0.038    267
  Dihedral  :  9.596  42.499    606
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.85 (0.50), residues: 198
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.40 (0.38), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG E 349 
 TYR   0.068   0.019   TYR C 310 
 PHE   0.042   0.021   PHE A 346 
 HIS   0.005   0.002   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.01077 ( 1569)
  covalent geometry    : angle       1.77711 ( 2097)
  hydrogen bonds       : bond        0.06114 (   33)
  hydrogen bonds       : angle       7.15680 (   99)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.058 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 LYS cc_start: 0.8115 (mttt) cc_final: 0.7912 (mtpt)
REVERT: A  347 LYS cc_start: 0.8466 (mttt) cc_final: 0.7559 (pmtt)
REVERT: A  369 LYS cc_start: 0.8309 (ttmt) cc_final: 0.7992 (ttpt)
REVERT: A  375 LYS cc_start: 0.7146 (tptm) cc_final: 0.6860 (tptt)
REVERT: C  340 LYS cc_start: 0.7413 (mttt) cc_final: 0.7164 (ttmm)
REVERT: C  345 ASP cc_start: 0.7491 (m-30) cc_final: 0.7001 (t70)
REVERT: C  347 LYS cc_start: 0.8400 (mttt) cc_final: 0.8141 (mtpt)
REVERT: C  349 ARG cc_start: 0.7573 (mtt180) cc_final: 0.6532 (mtt-85)
REVERT: E  320 SER cc_start: 0.8567 (m) cc_final: 0.8255 (p)
REVERT: E  321 LYS cc_start: 0.7395 (tttt) cc_final: 0.7089 (ttmp)
REVERT: E  340 LYS cc_start: 0.7549 (mttt) cc_final: 0.7296 (ttmm)
REVERT: E  369 LYS cc_start: 0.7591 (ttmt) cc_final: 0.7330 (ttpt)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 1.1581
  time to fit residues: 84.2772
Evaluate side-chains
  49 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 327 ASN
C 336 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.119840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.111055 restraints weight = 6479.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3887 rms_B_bonded: 1.86
r_work: 0.3792 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3704 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.3777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   1569  Z= 0.128
  Angle     :  0.610   3.994   2097  Z= 0.311
  Chirality :  0.052   0.137    234
  Planarity :  0.004   0.030    267
  Dihedral  :  6.200  16.978    207
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 1.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 11.30 %
    Favored  : 85.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.27 (0.51), residues: 198
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.96 (0.39), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.010   0.002   TYR E 310 
 PHE   0.007   0.002   PHE E 346 
 HIS   0.003   0.001   HIS E 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 1569)
  covalent geometry    : angle       0.60982 ( 2097)
  hydrogen bonds       : bond        0.02484 (   33)
  hydrogen bonds       : angle       4.84810 (   99)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 LYS cc_start: 0.8693 (mttt) cc_final: 0.7856 (pmtt)
REVERT: C  345 ASP cc_start: 0.7960 (m-30) cc_final: 0.7568 (t0)
REVERT: C  349 ARG cc_start: 0.8283 (mtt180) cc_final: 0.7033 (mtt-85)
REVERT: C  375 LYS cc_start: 0.6518 (OUTLIER) cc_final: 0.5201 (tmmt)
REVERT: E  340 LYS cc_start: 0.8209 (mttt) cc_final: 0.7971 (ttmm)
REVERT: E  347 LYS cc_start: 0.8574 (mttt) cc_final: 0.8364 (mptp)
  outliers start: 5
  outliers final: 1
  residues processed: 55
  average time/residue: 1.4110
  time to fit residues: 78.3927
Evaluate side-chains
  45 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  370 LYS
Chi-restraints excluded: chain C residue  375 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.121281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.113285 restraints weight = 6295.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3899 rms_B_bonded: 1.71
r_work: 0.3814 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3732 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.4799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   1569  Z= 0.108
  Angle     :  0.544   4.954   2097  Z= 0.268
  Chirality :  0.052   0.131    234
  Planarity :  0.003   0.022    267
  Dihedral  :  5.402  14.518    207
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 1.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 16.38 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.52), residues: 198
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.69 (0.40), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG E 349 
 TYR   0.010   0.002   TYR E 310 
 PHE   0.005   0.001   PHE C 346 
 HIS   0.002   0.000   HIS C 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 1569)
  covalent geometry    : angle       0.54449 ( 2097)
  hydrogen bonds       : bond        0.01761 (   33)
  hydrogen bonds       : angle       4.31816 (   99)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 LYS cc_start: 0.8687 (mttt) cc_final: 0.7790 (pmtt)
REVERT: C  345 ASP cc_start: 0.7917 (m-30) cc_final: 0.7646 (t0)
REVERT: C  349 ARG cc_start: 0.8346 (mtt180) cc_final: 0.7209 (mtt-85)
REVERT: C  375 LYS cc_start: 0.6606 (OUTLIER) cc_final: 0.5337 (tmmt)
REVERT: E  349 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7366 (mtt180)
  outliers start: 5
  outliers final: 2
  residues processed: 46
  average time/residue: 1.4664
  time to fit residues: 68.0927
Evaluate side-chains
  42 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  370 LYS
Chi-restraints excluded: chain C residue  375 LYS
Chi-restraints excluded: chain E residue  321 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
C 336 GLN
E 327 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.121091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.113010 restraints weight = 6156.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3890 rms_B_bonded: 1.69
r_work: 0.3813 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3733 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.5185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   1569  Z= 0.099
  Angle     :  0.514   4.684   2097  Z= 0.251
  Chirality :  0.052   0.126    234
  Planarity :  0.002   0.016    267
  Dihedral  :  4.938  14.108    207
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 18.08 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.69 (0.54), residues: 198
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.52 (0.41), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 349 
 TYR   0.008   0.002   TYR E 310 
 PHE   0.007   0.001   PHE E 346 
 HIS   0.003   0.001   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 1569)
  covalent geometry    : angle       0.51414 ( 2097)
  hydrogen bonds       : bond        0.01427 (   33)
  hydrogen bonds       : angle       3.90892 (   99)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.065 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  345 ASP cc_start: 0.7891 (m-30) cc_final: 0.7674 (t0)
REVERT: C  349 ARG cc_start: 0.8360 (mtt180) cc_final: 0.7194 (mtt-85)
REVERT: C  375 LYS cc_start: 0.6610 (OUTLIER) cc_final: 0.5443 (tmmt)
REVERT: E  349 ARG cc_start: 0.8014 (mtm180) cc_final: 0.7426 (mtt180)
  outliers start: 5
  outliers final: 1
  residues processed: 41
  average time/residue: 1.4479
  time to fit residues: 59.9323
Evaluate side-chains
  39 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  375 LYS
Chi-restraints excluded: chain E residue  321 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 0 optimal weight:    0.5980
   chunk 15 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.119006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.111115 restraints weight = 6449.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3876 rms_B_bonded: 1.70
r_work: 0.3799 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3722 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8605
moved from start:          0.5361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   1569  Z= 0.112
  Angle     :  0.522   4.843   2097  Z= 0.252
  Chirality :  0.051   0.125    234
  Planarity :  0.002   0.018    267
  Dihedral  :  4.812  13.439    207
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 1.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 19.21 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.55), residues: 198
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.43 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 349 
 TYR   0.008   0.002   TYR E 310 
 PHE   0.006   0.001   PHE E 346 
 HIS   0.002   0.001   HIS C 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 1569)
  covalent geometry    : angle       0.52199 ( 2097)
  hydrogen bonds       : bond        0.01290 (   33)
  hydrogen bonds       : angle       3.73600 (   99)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  345 ASP cc_start: 0.7882 (m-30) cc_final: 0.7670 (t0)
REVERT: C  349 ARG cc_start: 0.8330 (mtt180) cc_final: 0.7187 (mtt-85)
REVERT: C  375 LYS cc_start: 0.6669 (OUTLIER) cc_final: 0.5511 (tmmt)
REVERT: E  349 ARG cc_start: 0.8036 (mtm180) cc_final: 0.7510 (mtt180)
REVERT: E  358 ASP cc_start: 0.8303 (t0) cc_final: 0.8094 (t0)
  outliers start: 6
  outliers final: 2
  residues processed: 39
  average time/residue: 1.3752
  time to fit residues: 54.1679
Evaluate side-chains
  39 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  375 LYS
Chi-restraints excluded: chain E residue  321 LYS
Chi-restraints excluded: chain E residue  347 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0980
   chunk 4 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.6982

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.120605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.112327 restraints weight = 6620.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3892 rms_B_bonded: 1.79
r_work: 0.3810 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3731 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.5495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   1569  Z= 0.092
  Angle     :  0.502   4.654   2097  Z= 0.243
  Chirality :  0.052   0.125    234
  Planarity :  0.002   0.017    267
  Dihedral  :  4.585  12.439    207
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 1.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 19.21 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.54 (0.55), residues: 198
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.40 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 349 
 TYR   0.007   0.002   TYR E 310 
 PHE   0.003   0.001   PHE E 346 
 HIS   0.002   0.001   HIS C 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 1569)
  covalent geometry    : angle       0.50236 ( 2097)
  hydrogen bonds       : bond        0.01185 (   33)
  hydrogen bonds       : angle       3.60606 (   99)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.069 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  345 ASP cc_start: 0.7879 (m-30) cc_final: 0.7596 (t70)
REVERT: C  349 ARG cc_start: 0.8308 (mtt180) cc_final: 0.7157 (mtt-85)
REVERT: C  375 LYS cc_start: 0.6582 (OUTLIER) cc_final: 0.5430 (tmmt)
REVERT: E  347 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8345 (mmtm)
REVERT: E  349 ARG cc_start: 0.7976 (mtm180) cc_final: 0.7513 (mtt180)
  outliers start: 5
  outliers final: 2
  residues processed: 38
  average time/residue: 1.4057
  time to fit residues: 53.9208
Evaluate side-chains
  39 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  348 ASP
Chi-restraints excluded: chain C residue  375 LYS
Chi-restraints excluded: chain E residue  321 LYS
Chi-restraints excluded: chain E residue  347 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0470
   chunk 7 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.9082

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.120148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.112131 restraints weight = 6526.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3890 rms_B_bonded: 1.74
r_work: 0.3807 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3729 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.5606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   1569  Z= 0.106
  Angle     :  0.524   4.738   2097  Z= 0.251
  Chirality :  0.051   0.123    234
  Planarity :  0.003   0.019    267
  Dihedral  :  4.557  12.499    207
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 1.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 19.21 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.52 (0.55), residues: 198
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.39 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 349 
 TYR   0.010   0.002   TYR E 310 
 PHE   0.004   0.001   PHE E 346 
 HIS   0.003   0.001   HIS C 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 1569)
  covalent geometry    : angle       0.52447 ( 2097)
  hydrogen bonds       : bond        0.01191 (   33)
  hydrogen bonds       : angle       3.56953 (   99)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  345 ASP cc_start: 0.7863 (m-30) cc_final: 0.7656 (t70)
REVERT: C  349 ARG cc_start: 0.8332 (mtt180) cc_final: 0.7237 (mtt-85)
REVERT: C  375 LYS cc_start: 0.6633 (OUTLIER) cc_final: 0.5498 (tmmt)
REVERT: E  349 ARG cc_start: 0.8052 (mtm180) cc_final: 0.7633 (mtt180)
  outliers start: 4
  outliers final: 3
  residues processed: 37
  average time/residue: 1.3936
  time to fit residues: 52.1394
Evaluate side-chains
  38 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  348 ASP
Chi-restraints excluded: chain C residue  375 LYS
Chi-restraints excluded: chain E residue  321 LYS
Chi-restraints excluded: chain E residue  347 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.118655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.110659 restraints weight = 6353.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3857 rms_B_bonded: 1.72
r_work: 0.3773 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.3695 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.5676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   1569  Z= 0.129
  Angle     :  0.541   5.328   2097  Z= 0.262
  Chirality :  0.051   0.123    234
  Planarity :  0.003   0.018    267
  Dihedral  :  4.603  12.465    207
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 19.77 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.56 (0.55), residues: 198
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.42 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 349 
 TYR   0.013   0.003   TYR C 310 
 PHE   0.005   0.001   PHE E 346 
 HIS   0.003   0.001   HIS C 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 1569)
  covalent geometry    : angle       0.54078 ( 2097)
  hydrogen bonds       : bond        0.01174 (   33)
  hydrogen bonds       : angle       3.53174 (   99)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.057 
Fit side-chains
   revert: symmetry clash
REVERT: C  345 ASP cc_start: 0.7860 (m-30) cc_final: 0.7659 (t70)
REVERT: C  349 ARG cc_start: 0.8342 (mtt180) cc_final: 0.7388 (mtt-85)
REVERT: C  375 LYS cc_start: 0.6624 (OUTLIER) cc_final: 0.5520 (tmmt)
REVERT: E  349 ARG cc_start: 0.8056 (mtm180) cc_final: 0.7652 (mtt180)
  outliers start: 4
  outliers final: 2
  residues processed: 36
  average time/residue: 1.2887
  time to fit residues: 46.8933
Evaluate side-chains
  34 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  348 ASP
Chi-restraints excluded: chain C residue  375 LYS
Chi-restraints excluded: chain E residue  321 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 13 optimal weight:    4.9990
   chunk 7 optimal weight:    0.7980
   chunk 0 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.9382

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.119156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.110886 restraints weight = 6490.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3865 rms_B_bonded: 1.80
r_work: 0.3781 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3701 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.5950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   1569  Z= 0.108
  Angle     :  0.554   5.815   2097  Z= 0.263
  Chirality :  0.051   0.124    234
  Planarity :  0.003   0.022    267
  Dihedral  :  4.518  12.045    207
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 20.90 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.57 (0.55), residues: 198
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.43 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG C 349 
 TYR   0.009   0.002   TYR C 310 
 PHE   0.003   0.001   PHE E 346 
 HIS   0.002   0.001   HIS C 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 1569)
  covalent geometry    : angle       0.55375 ( 2097)
  hydrogen bonds       : bond        0.01185 (   33)
  hydrogen bonds       : angle       3.45647 (   99)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.071 
Fit side-chains
   revert: symmetry clash
REVERT: C  345 ASP cc_start: 0.7842 (m-30) cc_final: 0.7602 (t70)
REVERT: C  349 ARG cc_start: 0.8331 (mtt180) cc_final: 0.7317 (mtt-85)
REVERT: C  375 LYS cc_start: 0.6725 (OUTLIER) cc_final: 0.5604 (tmmt)
REVERT: E  349 ARG cc_start: 0.8049 (mtm180) cc_final: 0.7583 (mtt180)
  outliers start: 3
  outliers final: 2
  residues processed: 32
  average time/residue: 1.3527
  time to fit residues: 43.8078
Evaluate side-chains
  34 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  348 ASP
Chi-restraints excluded: chain C residue  375 LYS
Chi-restraints excluded: chain E residue  321 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.119545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.111285 restraints weight = 6455.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3865 rms_B_bonded: 1.80
r_work: 0.3783 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3704 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.5940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   1569  Z= 0.107
  Angle     :  0.548   6.229   2097  Z= 0.260
  Chirality :  0.051   0.123    234
  Planarity :  0.003   0.024    267
  Dihedral  :  4.478  11.874    207
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 20.34 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.55), residues: 198
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.43 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG E 349 
 TYR   0.009   0.002   TYR C 310 
 PHE   0.003   0.001   PHE E 346 
 HIS   0.002   0.001   HIS C 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 1569)
  covalent geometry    : angle       0.54796 ( 2097)
  hydrogen bonds       : bond        0.01343 (   33)
  hydrogen bonds       : angle       3.46238 (   99)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.057 
Fit side-chains
   revert: symmetry clash
REVERT: C  345 ASP cc_start: 0.7834 (m-30) cc_final: 0.7608 (t70)
REVERT: C  349 ARG cc_start: 0.8322 (mtt180) cc_final: 0.7331 (mtt-85)
REVERT: E  349 ARG cc_start: 0.8017 (mtm180) cc_final: 0.7579 (mtt180)
  outliers start: 3
  outliers final: 2
  residues processed: 32
  average time/residue: 1.3014
  time to fit residues: 42.1143
Evaluate side-chains
  31 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 29
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  348 ASP
Chi-restraints excluded: chain E residue  321 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.118702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.110842 restraints weight = 6588.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 1.75
r_work: 0.3768 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3689 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.5934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   1569  Z= 0.108
  Angle     :  0.547   6.160   2097  Z= 0.259
  Chirality :  0.051   0.123    234
  Planarity :  0.003   0.024    267
  Dihedral  :  4.465  11.677    207
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 1.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 21.47 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.55), residues: 198
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.44 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG C 349 
 TYR   0.009   0.002   TYR C 310 
 PHE   0.003   0.001   PHE E 346 
 HIS   0.004   0.001   HIS C 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 1569)
  covalent geometry    : angle       0.54711 ( 2097)
  hydrogen bonds       : bond        0.01361 (   33)
  hydrogen bonds       : angle       3.47620 (   99)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1873.93 seconds
wall clock time: 32 minutes 25.47 seconds (1945.47 seconds total)