Starting phenix.real_space_refine
on Wed Jun  3 10:01:51 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9r88_53807/06_2026/9r88_53807.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9r88_53807/06_2026/9r88_53807.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9r88_53807/06_2026/9r88_53807.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9r88_53807/06_2026/9r88_53807.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9r88_53807/06_2026/9r88_53807.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9r88_53807/06_2026/9r88_53807.cif"
  }
  resolution = 2.6
  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: 4
    Type Number    sf(0)   Gaussians
     S       5      5.16       5
     C    1800      2.51       5
     N     530      2.21       5
     O     535      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2870
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 0.63, per 1000 atoms: 0.22
  Number of scatterers: 2870
  At special positions: 0
  Unit cell: (140.904, 126.072, 32.136, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       5     16.00
     O     535      8.00
     N     530      7.00
     C    1800      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.22
  Conformation dependent library (CDL) restraints added in 113.4 milliseconds
  

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  660

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 20 sheets defined
      0.0% alpha, 44.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310
      removed outlier: 6.347A  pdb=" N   GLN A 307 " --> pdb=" O   ILE B 308 " (cutoff:3.500A)
      removed outlier: 7.901A  pdb=" N   TYR B 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   VAL A 309 " --> pdb=" O   TYR B 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314
      removed outlier: 6.840A  pdb=" N   VAL A 313 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 322
      removed outlier: 6.295A  pdb=" N   LYS A 317 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   SER B 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   THR A 319 " --> pdb=" O   SER B 320 " (cutoff:3.500A)
      removed outlier: 8.431A  pdb=" N   CYS B 322 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   LYS A 321 " --> pdb=" O   CYS B 322 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 325 through 330
      removed outlier: 8.492A  pdb=" N   LEU A 325 " --> pdb=" O   GLY B 326 " (cutoff:3.500A)
      removed outlier: 9.390A  pdb=" N   ILE B 328 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ASN A 327 " --> pdb=" O   ILE B 328 " (cutoff:3.500A)
      removed outlier: 7.940A  pdb=" N   HIS B 330 " --> pdb=" O   ASN A 327 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   HIS A 329 " --> pdb=" O   HIS B 330 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   GLY A 326 " --> pdb=" O   LEU E 325 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   ASN E 327 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 339
      removed outlier: 6.496A  pdb=" N   VAL A 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 345 through 346
      removed outlier: 6.068A  pdb=" N   ASP A 345 " --> pdb=" O   PHE B 346 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 350 through 357
      removed outlier: 6.349A  pdb=" N   GLN A 351 " --> pdb=" O   SER B 352 " (cutoff:3.500A)
      removed outlier: 8.059A  pdb=" N   ILE B 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   LYS A 353 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   SER B 356 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   GLY A 355 " --> pdb=" O   SER B 356 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 360 through 362
      removed outlier: 6.347A  pdb=" N   THR A 361 " --> pdb=" O   HIS E 362 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 369 through 373
      removed outlier: 6.693A  pdb=" N   LYS A 369 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
      removed outlier: 8.250A  pdb=" N   GLU B 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   ILE A 371 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 376 through 378
      removed outlier: 6.283A  pdb=" N   THR A 377 " --> pdb=" O   PHE B 378 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 306 through 310
    Processing sheet with id=AB3, first strand: chain 'C' and resid 313 through 314
    Processing sheet with id=AB4, first strand: chain 'C' and resid 317 through 322
    Processing sheet with id=AB5, first strand: chain 'C' and resid 325 through 330
      removed outlier: 6.823A  pdb=" N   GLY C 326 " --> pdb=" O   LEU D 325 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   ASN D 327 " --> pdb=" O   GLY C 326 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 337 through 339
      removed outlier: 6.496A  pdb=" N   VAL C 337 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'C' and resid 345 through 346
    Processing sheet with id=AB8, first strand: chain 'C' and resid 350 through 357
    Processing sheet with id=AB9, first strand: chain 'C' and resid 360 through 362
      removed outlier: 6.348A  pdb=" N   THR C 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9
    Processing sheet with id=AC1, first strand: chain 'C' and resid 369 through 373
    Processing sheet with id=AC2, first strand: chain 'C' and resid 376 through 378

    58 hydrogen bonds defined for protein.
    174 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: 0.39

  Time building geometry restraints manager: 0.30 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 633
        1.33 -     1.45: 585
        1.45 -     1.57: 1692
        1.57 -     1.68: 0
        1.68 -     1.80: 5
  Bond restraints: 2915
  Sorted by residual:
  bond pdb=" CG  HIS B 330 "
       pdb=" CD2 HIS B 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.303  0.051 1.10e-02 8.26e+03 2.14e+01
  bond pdb=" CG  HIS A 330 "
       pdb=" CD2 HIS A 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.303  0.051 1.10e-02 8.26e+03 2.14e+01
  bond pdb=" CG  HIS C 330 "
       pdb=" CD2 HIS C 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.303  0.051 1.10e-02 8.26e+03 2.11e+01
  bond pdb=" CG  HIS E 330 "
       pdb=" CD2 HIS E 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.304  0.050 1.10e-02 8.26e+03 2.10e+01
  bond pdb=" CG  HIS D 330 "
       pdb=" CD2 HIS D 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.304  0.050 1.10e-02 8.26e+03 2.09e+01
  ... (remaining 2910 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 2692
        1.58 -     3.15: 864
        3.15 -     4.73: 268
        4.73 -     6.31: 51
        6.31 -     7.88: 25
  Bond angle restraints: 3900
  Sorted by residual:
  angle pdb=" CA  ASP C 314 "
        pdb=" CB  ASP C 314 "
        pdb=" CG  ASP C 314 "
      ideal   model   delta    sigma   weight residual
     112.60  117.69   -5.09 1.00e+00 1.00e+00 2.59e+01
  angle pdb=" CA  ASP B 314 "
        pdb=" CB  ASP B 314 "
        pdb=" CG  ASP B 314 "
      ideal   model   delta    sigma   weight residual
     112.60  117.68   -5.08 1.00e+00 1.00e+00 2.58e+01
  angle pdb=" CA  ASP A 314 "
        pdb=" CB  ASP A 314 "
        pdb=" CG  ASP A 314 "
      ideal   model   delta    sigma   weight residual
     112.60  117.66   -5.06 1.00e+00 1.00e+00 2.56e+01
  angle pdb=" CA  ASP E 314 "
        pdb=" CB  ASP E 314 "
        pdb=" CG  ASP E 314 "
      ideal   model   delta    sigma   weight residual
     112.60  117.66   -5.06 1.00e+00 1.00e+00 2.56e+01
  angle pdb=" CA  ASP D 314 "
        pdb=" CB  ASP D 314 "
        pdb=" CG  ASP D 314 "
      ideal   model   delta    sigma   weight residual
     112.60  117.63   -5.03 1.00e+00 1.00e+00 2.53e+01
  ... (remaining 3895 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.00: 1705
       17.00 -    33.99: 60
       33.99 -    50.99: 10
       50.99 -    67.99: 0
       67.99 -    84.99: 5
  Dihedral angle restraints: 1780
    sinusoidal: 745
      harmonic: 1035
  Sorted by residual:
  dihedral pdb=" CA  VAL B 318 "
           pdb=" C   VAL B 318 "
           pdb=" N   THR B 319 "
           pdb=" CA  THR B 319 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.14  -18.86     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  VAL A 318 "
           pdb=" C   VAL A 318 "
           pdb=" N   THR A 319 "
           pdb=" CA  THR A 319 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.15  -18.85     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  VAL D 318 "
           pdb=" C   VAL D 318 "
           pdb=" N   THR D 319 "
           pdb=" CA  THR D 319 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.15  -18.85     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 1777 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.050: 191
       0.050 -    0.098: 124
       0.098 -    0.147: 86
       0.147 -    0.195: 19
       0.195 -    0.244: 20
  Chirality restraints: 440
  Sorted by residual:
  chirality pdb=" CA  ASN D 327 "
            pdb=" N   ASN D 327 "
            pdb=" C   ASN D 327 "
            pdb=" CB  ASN D 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.49e+00
  chirality pdb=" CA  ASN A 327 "
            pdb=" N   ASN A 327 "
            pdb=" C   ASN A 327 "
            pdb=" CB  ASN A 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CA  ASN E 327 "
            pdb=" N   ASN E 327 "
            pdb=" C   ASN E 327 "
            pdb=" CB  ASN E 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.47e+00
  ... (remaining 437 not shown)

  Planarity restraints: 495
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS E 362 "    0.018 2.00e-02 2.50e+03   1.71e-02 4.40e+00
        pdb=" CG  HIS E 362 "   -0.036 2.00e-02 2.50e+03
        pdb=" ND1 HIS E 362 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 HIS E 362 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 HIS E 362 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE2 HIS E 362 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 362 "    0.017 2.00e-02 2.50e+03   1.71e-02 4.38e+00
        pdb=" CG  HIS B 362 "   -0.036 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 362 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 362 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 362 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 362 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 362 "    0.018 2.00e-02 2.50e+03   1.70e-02 4.36e+00
        pdb=" CG  HIS A 362 "   -0.036 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 362 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 362 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 362 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 362 "    0.009 2.00e-02 2.50e+03
  ... (remaining 492 not shown)

  Histogram of nonbonded interaction distances:
        2.57 -     3.04: 1595
        3.04 -     3.50: 2609
        3.50 -     3.97: 4168
        3.97 -     4.43: 4355
        4.43 -     4.90: 8835
  Nonbonded interactions: 21562
  Sorted by model distance:
  nonbonded pdb=" ND1 HIS A 330 "
            pdb=" OG1 THR B 361 "
     model   vdw
     2.569 3.120
  nonbonded pdb=" OG1 THR C 361 "
            pdb=" ND1 HIS D 330 "
     model   vdw
     2.570 3.120
  nonbonded pdb=" OG1 THR A 361 "
            pdb=" ND1 HIS E 330 "
     model   vdw
     2.570 3.120
  nonbonded pdb=" OH  TYR C 310 "
            pdb=" ND1 HIS C 374 "
     model   vdw
     2.582 3.120
  nonbonded pdb=" OH  TYR E 310 "
            pdb=" ND1 HIS E 374 "
     model   vdw
     2.582 3.120
  ... (remaining 21557 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  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:             4.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     4.370
  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:5.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8898
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   0.058   2915  Z= 0.708
  Angle     :  1.824   7.884   3900  Z= 1.151
  Chirality :  0.089   0.244    440
  Planarity :  0.008   0.027    495
  Dihedral  : 10.812  84.985   1120
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.82 (0.31), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.23), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.002   ARG E 349 
 TYR   0.014   0.007   TYR E 310 
 PHE   0.012   0.005   PHE D 378 
 HIS   0.016   0.006   HIS E 362 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01091 /  0.71 ( 2915)
  covalent geometry    : angle       1.82439 /  1.15 ( 3900)
  hydrogen bonds       : bond        0.14064 /  8.96 (   58)
  hydrogen bonds       : angle       6.56393 /  4.25 (  174)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A  331 LYS cc_start: 0.8958 (mtpt) cc_final: 0.8713 (mtmm)
REVERT: A  338 GLU cc_start: 0.9050 (tt0) cc_final: 0.8832 (tm-30)
REVERT: B  331 LYS cc_start: 0.9025 (mtpt) cc_final: 0.8794 (mttm)
REVERT: B  349 ARG cc_start: 0.9001 (mtt180) cc_final: 0.7518 (ptt-90)
REVERT: C  331 LYS cc_start: 0.9010 (mtpt) cc_final: 0.8782 (mtmm)
REVERT: C  349 ARG cc_start: 0.8998 (mtt180) cc_final: 0.7592 (ptt-90)
REVERT: D  321 LYS cc_start: 0.9070 (mtpt) cc_final: 0.8868 (mtmt)
REVERT: D  331 LYS cc_start: 0.9005 (mtpt) cc_final: 0.8749 (mttm)
REVERT: D  338 GLU cc_start: 0.8997 (tt0) cc_final: 0.8795 (tm-30)
REVERT: D  349 ARG cc_start: 0.9021 (mtt180) cc_final: 0.7769 (mmp-170)
REVERT: E  338 GLU cc_start: 0.9055 (tt0) cc_final: 0.8813 (tm-30)
REVERT: E  349 ARG cc_start: 0.9022 (mtt180) cc_final: 0.7937 (mmp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.7853
  time to fit residues: 103.6839
Evaluate side-chains
  71 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    8.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 362 HIS
B 307 GLN
** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 351 GLN
B 362 HIS
C 330 HIS
C 362 HIS
D 362 HIS
E 351 GLN
E 362 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.138353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.122408 restraints weight = 3303.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3870 rms_B_bonded: 1.90
r_work: 0.3757 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3659 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8762
moved from start:          0.2765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2915  Z= 0.160
  Angle     :  0.679   6.105   3900  Z= 0.330
  Chirality :  0.051   0.139    440
  Planarity :  0.003   0.033    495
  Dihedral  :  4.709  15.907    385
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 16.97 %
    Favored  : 80.00 %
  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: -2.29 (0.33), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.25), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 379 
 TYR   0.024   0.003   TYR B 310 
 PHE   0.013   0.002   PHE D 378 
 HIS   0.008   0.002   HIS D 330 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00381 /  0.16 ( 2915)
  covalent geometry    : angle       0.67912 /  0.33 ( 3900)
  hydrogen bonds       : bond        0.02434 /  1.55 (   58)
  hydrogen bonds       : angle       5.18258 /  3.52 (  174)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A  338 GLU cc_start: 0.8429 (tt0) cc_final: 0.8117 (tm-30)
REVERT: A  349 ARG cc_start: 0.8458 (mtp180) cc_final: 0.8196 (mtp85)
REVERT: B  338 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8411 (tm-30)
REVERT: B  349 ARG cc_start: 0.8518 (mtt180) cc_final: 0.6951 (pmt-80)
REVERT: C  349 ARG cc_start: 0.8456 (mtt180) cc_final: 0.6825 (pmt-80)
REVERT: C  379 ARG cc_start: 0.8001 (ttm110) cc_final: 0.7168 (mtt-85)
REVERT: D  321 LYS cc_start: 0.8584 (mtpt) cc_final: 0.8346 (mtmt)
REVERT: D  338 GLU cc_start: 0.8424 (tt0) cc_final: 0.8104 (tm-30)
REVERT: D  349 ARG cc_start: 0.8376 (mtt180) cc_final: 0.6928 (mmp-170)
REVERT: E  321 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.7924 (mtmt)
REVERT: E  338 GLU cc_start: 0.8520 (tt0) cc_final: 0.8196 (tm-30)
REVERT: E  349 ARG cc_start: 0.8451 (mtt180) cc_final: 0.7025 (mmp-170)
  outliers start: 10
  outliers final: 5
  residues processed: 91
  average time/residue: 0.6270
  time to fit residues: 58.2251
Evaluate side-chains
  85 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  336 GLN
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain E residue  321 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 22 optimal weight:    9.9990
   chunk 23 optimal weight:    9.9990
   chunk 19 optimal weight:    8.9990
   chunk 32 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 30 optimal weight:   10.0000
   chunk 12 optimal weight:    5.9990
   chunk 25 optimal weight:    8.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.127528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.111766 restraints weight = 3415.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 1.86
r_work: 0.3624 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3529 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8881
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.044   2915  Z= 0.367
  Angle     :  0.827   4.922   3900  Z= 0.424
  Chirality :  0.055   0.155    440
  Planarity :  0.003   0.019    495
  Dihedral  :  5.482  18.799    385
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 18.18 %
    Favored  : 76.97 %
  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 are not related in a simple way.
  whole: -2.15 (0.35), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.63 (0.26), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.002   ARG B 379 
 TYR   0.014   0.002   TYR B 310 
 PHE   0.015   0.003   PHE D 378 
 HIS   0.012   0.002   HIS D 330 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00890 /  0.37 ( 2915)
  covalent geometry    : angle       0.82662 /  0.42 ( 3900)
  hydrogen bonds       : bond        0.02879 /  1.83 (   58)
  hydrogen bonds       : angle       5.26125 /  3.50 (  174)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A  338 GLU cc_start: 0.8483 (tt0) cc_final: 0.8070 (tm-30)
REVERT: A  349 ARG cc_start: 0.8478 (mtp180) cc_final: 0.7957 (mtt180)
REVERT: B  338 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8443 (tm-30)
REVERT: B  349 ARG cc_start: 0.8598 (mtt180) cc_final: 0.7014 (pmt-80)
REVERT: B  379 ARG cc_start: 0.8174 (ttm110) cc_final: 0.7284 (mtt180)
REVERT: C  325 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9185 (tp)
REVERT: C  349 ARG cc_start: 0.8500 (mtt180) cc_final: 0.6831 (ptt-90)
REVERT: D  321 LYS cc_start: 0.8713 (mtpt) cc_final: 0.8431 (mtmt)
REVERT: D  338 GLU cc_start: 0.8469 (tt0) cc_final: 0.8094 (tm-30)
REVERT: D  349 ARG cc_start: 0.8398 (mtt180) cc_final: 0.7093 (mmt-90)
REVERT: E  338 GLU cc_start: 0.8549 (tt0) cc_final: 0.8176 (tm-30)
REVERT: E  349 ARG cc_start: 0.8478 (mtt180) cc_final: 0.7138 (mtt-85)
  outliers start: 16
  outliers final: 4
  residues processed: 91
  average time/residue: 0.6495
  time to fit residues: 60.2463
Evaluate side-chains
  85 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  338 GLU
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain D residue  306 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   chunk 3 optimal weight:    9.9990
   chunk 0 optimal weight:    3.9990
   chunk 27 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 21 optimal weight:    8.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 351 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.130254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.115139 restraints weight = 3334.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 1.83
r_work: 0.3659 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3565 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8863
moved from start:          0.3780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   2915  Z= 0.204
  Angle     :  0.668   5.020   3900  Z= 0.335
  Chirality :  0.050   0.139    440
  Planarity :  0.004   0.061    495
  Dihedral  :  5.187  17.472    385
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 21.21 %
    Favored  : 76.36 %
  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: -1.99 (0.35), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.51 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG C 379 
 TYR   0.029   0.004   TYR D 310 
 PHE   0.014   0.002   PHE A 346 
 HIS   0.007   0.001   HIS D 330 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00496 /  0.20 ( 2915)
  covalent geometry    : angle       0.66779 /  0.34 ( 3900)
  hydrogen bonds       : bond        0.02279 /  1.47 (   58)
  hydrogen bonds       : angle       5.06310 /  3.40 (  174)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.077 
Fit side-chains
REVERT: A  338 GLU cc_start: 0.8465 (tt0) cc_final: 0.8065 (tm-30)
REVERT: A  349 ARG cc_start: 0.8484 (mtp180) cc_final: 0.8019 (mtt180)
REVERT: A  379 ARG cc_start: 0.7485 (mtt180) cc_final: 0.7200 (mtt-85)
REVERT: B  338 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8406 (tm-30)
REVERT: B  349 ARG cc_start: 0.8621 (mtt180) cc_final: 0.7078 (pmt-80)
REVERT: C  349 ARG cc_start: 0.8513 (mtt180) cc_final: 0.6863 (pmt-80)
REVERT: C  379 ARG cc_start: 0.7983 (ttm110) cc_final: 0.7332 (mtt180)
REVERT: D  311 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.7939 (mttm)
REVERT: D  321 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8376 (mtmt)
REVERT: D  338 GLU cc_start: 0.8466 (tt0) cc_final: 0.8098 (tm-30)
REVERT: D  349 ARG cc_start: 0.8383 (mtt180) cc_final: 0.7072 (mmt-90)
REVERT: E  338 GLU cc_start: 0.8525 (tt0) cc_final: 0.8188 (tm-30)
REVERT: E  349 ARG cc_start: 0.8509 (mtt180) cc_final: 0.7031 (mmp-170)
REVERT: E  379 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7448 (mmt180)
  outliers start: 8
  outliers final: 5
  residues processed: 86
  average time/residue: 0.6636
  time to fit residues: 58.1265
Evaluate side-chains
  88 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  338 GLU
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain E residue  379 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 13 optimal weight:    0.4980
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    9.9990
   chunk 10 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 27 optimal weight:    0.6980
   chunk 34 optimal weight:    5.9990
   chunk 21 optimal weight:    7.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 368 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.135242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.120567 restraints weight = 3272.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3841 rms_B_bonded: 1.81
r_work: 0.3730 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3637 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8806
moved from start:          0.3933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   2915  Z= 0.101
  Angle     :  0.558   4.808   3900  Z= 0.272
  Chirality :  0.048   0.123    440
  Planarity :  0.004   0.058    495
  Dihedral  :  4.642  14.151    385
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 21.82 %
    Favored  : 76.36 %
  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: -1.91 (0.36), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.45 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 379 
 TYR   0.025   0.003   TYR D 310 
 PHE   0.011   0.002   PHE B 378 
 HIS   0.005   0.001   HIS A 330 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.10 ( 2915)
  covalent geometry    : angle       0.55755 /  0.27 ( 3900)
  hydrogen bonds       : bond        0.01655 /  1.08 (   58)
  hydrogen bonds       : angle       4.78421 /  3.26 (  174)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A  338 GLU cc_start: 0.8456 (tt0) cc_final: 0.8039 (tm-30)
REVERT: A  349 ARG cc_start: 0.8489 (mtp180) cc_final: 0.8165 (mtp85)
REVERT: B  338 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8407 (tm-30)
REVERT: B  349 ARG cc_start: 0.8590 (mtt180) cc_final: 0.7016 (pmt-80)
REVERT: B  379 ARG cc_start: 0.8067 (ttm110) cc_final: 0.7137 (mtt180)
REVERT: C  349 ARG cc_start: 0.8498 (mtt180) cc_final: 0.6892 (pmt-80)
REVERT: C  379 ARG cc_start: 0.7966 (ttm110) cc_final: 0.7314 (mtt180)
REVERT: D  321 LYS cc_start: 0.8570 (mtpt) cc_final: 0.8349 (mtmt)
REVERT: D  338 GLU cc_start: 0.8477 (tt0) cc_final: 0.8098 (tm-30)
REVERT: D  349 ARG cc_start: 0.8355 (mtt180) cc_final: 0.6881 (mmp-170)
REVERT: D  379 ARG cc_start: 0.7423 (mmt180) cc_final: 0.6683 (mmt180)
REVERT: E  338 GLU cc_start: 0.8516 (tt0) cc_final: 0.8155 (tm-30)
REVERT: E  349 ARG cc_start: 0.8451 (mtt180) cc_final: 0.7082 (mmp80)
REVERT: E  379 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7375 (mmt180)
  outliers start: 6
  outliers final: 4
  residues processed: 84
  average time/residue: 0.6483
  time to fit residues: 55.5576
Evaluate side-chains
  84 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain E residue  379 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 8 optimal weight:    3.9990
   chunk 21 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0570
   chunk 9 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 12 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    1.5702

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.134497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.119189 restraints weight = 3331.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3813 rms_B_bonded: 1.91
r_work: 0.3698 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3604 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8831
moved from start:          0.3995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2915  Z= 0.109
  Angle     :  0.555   4.310   3900  Z= 0.272
  Chirality :  0.048   0.128    440
  Planarity :  0.003   0.043    495
  Dihedral  :  4.548  13.882    385
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 1.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 24.24 %
    Favored  : 73.64 %
  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: -1.85 (0.36), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.40 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 379 
 TYR   0.023   0.003   TYR D 310 
 PHE   0.011   0.002   PHE A 346 
 HIS   0.005   0.001   HIS A 330 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.11 ( 2915)
  covalent geometry    : angle       0.55488 /  0.27 ( 3900)
  hydrogen bonds       : bond        0.01605 /  1.05 (   58)
  hydrogen bonds       : angle       4.67861 /  3.19 (  174)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A  338 GLU cc_start: 0.8476 (tt0) cc_final: 0.8103 (tm-30)
REVERT: A  349 ARG cc_start: 0.8512 (mtp180) cc_final: 0.8264 (mtp85)
REVERT: B  338 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8416 (tm-30)
REVERT: B  349 ARG cc_start: 0.8650 (mtt180) cc_final: 0.7082 (pmt-80)
REVERT: B  379 ARG cc_start: 0.8119 (ttm110) cc_final: 0.7219 (mtt180)
REVERT: C  349 ARG cc_start: 0.8509 (mtt180) cc_final: 0.6899 (pmt-80)
REVERT: C  379 ARG cc_start: 0.7985 (ttm110) cc_final: 0.7392 (mtt180)
REVERT: D  321 LYS cc_start: 0.8620 (mtpt) cc_final: 0.8310 (mttt)
REVERT: D  338 GLU cc_start: 0.8502 (tt0) cc_final: 0.8136 (tm-30)
REVERT: D  349 ARG cc_start: 0.8373 (mtt180) cc_final: 0.7025 (mtt-85)
REVERT: D  379 ARG cc_start: 0.7446 (mmt180) cc_final: 0.6712 (mmt180)
REVERT: E  338 GLU cc_start: 0.8552 (tt0) cc_final: 0.8215 (tm-30)
REVERT: E  349 ARG cc_start: 0.8456 (mtt180) cc_final: 0.7048 (mmp80)
REVERT: E  379 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7412 (mmt180)
  outliers start: 7
  outliers final: 4
  residues processed: 82
  average time/residue: 0.6747
  time to fit residues: 56.4773
Evaluate side-chains
  83 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain E residue  379 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 21 optimal weight:    8.9990
   chunk 29 optimal weight:    9.9990
   chunk 23 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 9 optimal weight:   10.0000
   chunk 3 optimal weight:    4.9990
   chunk 20 optimal weight:    9.9990
   chunk 32 optimal weight:    9.9990
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.129106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.113692 restraints weight = 3378.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3740 rms_B_bonded: 1.86
r_work: 0.3625 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3531 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8869
moved from start:          0.3947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.032   2915  Z= 0.246
  Angle     :  0.661   4.991   3900  Z= 0.337
  Chirality :  0.050   0.142    440
  Planarity :  0.003   0.028    495
  Dihedral  :  5.038  16.823    385
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 24.24 %
    Favored  : 73.64 %
  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: -1.94 (0.36), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.47 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 379 
 TYR   0.021   0.003   TYR D 310 
 PHE   0.023   0.004   PHE E 346 
 HIS   0.008   0.001   HIS A 330 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00590 /  0.25 ( 2915)
  covalent geometry    : angle       0.66060 /  0.34 ( 3900)
  hydrogen bonds       : bond        0.02153 /  1.40 (   58)
  hydrogen bonds       : angle       4.90360 /  3.30 (  174)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A  338 GLU cc_start: 0.8497 (tt0) cc_final: 0.8066 (tm-30)
REVERT: A  349 ARG cc_start: 0.8472 (mtp180) cc_final: 0.7925 (mtt180)
REVERT: B  338 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8405 (tm-30)
REVERT: B  349 ARG cc_start: 0.8601 (mtt180) cc_final: 0.6959 (pmt-80)
REVERT: B  379 ARG cc_start: 0.8193 (ttm110) cc_final: 0.7237 (mtt180)
REVERT: C  349 ARG cc_start: 0.8529 (mtt180) cc_final: 0.6796 (pmt-80)
REVERT: D  321 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8362 (mttt)
REVERT: D  338 GLU cc_start: 0.8480 (tt0) cc_final: 0.8096 (tm-30)
REVERT: D  349 ARG cc_start: 0.8361 (mtt180) cc_final: 0.7028 (mtt-85)
REVERT: D  379 ARG cc_start: 0.7571 (mmt180) cc_final: 0.6810 (mmt180)
REVERT: E  338 GLU cc_start: 0.8547 (tt0) cc_final: 0.8170 (tm-30)
REVERT: E  349 ARG cc_start: 0.8477 (mtt180) cc_final: 0.6945 (mmp-170)
REVERT: E  379 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7445 (mmt180)
  outliers start: 7
  outliers final: 4
  residues processed: 80
  average time/residue: 0.6591
  time to fit residues: 53.7970
Evaluate side-chains
  82 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  338 GLU
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain E residue  379 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 18 optimal weight:    0.9990
   chunk 7 optimal weight:    0.1980
   chunk 20 optimal weight:    8.9990
   chunk 22 optimal weight:    8.9990
   chunk 5 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    3.0388

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.130458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.114986 restraints weight = 3416.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 1.91
r_work: 0.3641 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3547 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8870
moved from start:          0.4063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   2915  Z= 0.185
  Angle     :  0.627   5.880   3900  Z= 0.316
  Chirality :  0.049   0.137    440
  Planarity :  0.004   0.078    495
  Dihedral  :  5.007  16.458    385
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 24.85 %
    Favored  : 73.33 %
  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: -1.93 (0.36), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.46 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.002   ARG C 379 
 TYR   0.025   0.004   TYR E 310 
 PHE   0.016   0.003   PHE E 346 
 HIS   0.007   0.001   HIS A 330 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00446 /  0.18 ( 2915)
  covalent geometry    : angle       0.62678 /  0.32 ( 3900)
  hydrogen bonds       : bond        0.01986 /  1.28 (   58)
  hydrogen bonds       : angle       4.86414 /  3.28 (  174)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A  338 GLU cc_start: 0.8490 (tt0) cc_final: 0.8108 (tm-30)
REVERT: A  349 ARG cc_start: 0.8496 (mtp180) cc_final: 0.8229 (mtp85)
REVERT: B  338 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8421 (tm-30)
REVERT: B  349 ARG cc_start: 0.8631 (mtt180) cc_final: 0.7022 (pmt-80)
REVERT: B  379 ARG cc_start: 0.8209 (ttm110) cc_final: 0.7340 (mtt180)
REVERT: C  349 ARG cc_start: 0.8525 (mtt180) cc_final: 0.6831 (pmt-80)
REVERT: C  379 ARG cc_start: 0.8076 (ttm110) cc_final: 0.7379 (mtt180)
REVERT: D  321 LYS cc_start: 0.8667 (mtpt) cc_final: 0.8352 (mtpt)
REVERT: D  338 GLU cc_start: 0.8507 (tt0) cc_final: 0.8130 (tm-30)
REVERT: D  349 ARG cc_start: 0.8365 (mtt180) cc_final: 0.7077 (mtt-85)
REVERT: D  379 ARG cc_start: 0.7538 (mmt180) cc_final: 0.6819 (mmt180)
REVERT: E  338 GLU cc_start: 0.8550 (tt0) cc_final: 0.8201 (tm-30)
REVERT: E  349 ARG cc_start: 0.8494 (mtt180) cc_final: 0.7043 (mmp-170)
  outliers start: 6
  outliers final: 4
  residues processed: 78
  average time/residue: 0.6081
  time to fit residues: 48.4749
Evaluate side-chains
  80 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  338 GLU
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain D residue  306 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 2 optimal weight:    8.9990
   chunk 24 optimal weight:    9.9990
   chunk 14 optimal weight:    7.9990
   chunk 1 optimal weight:    6.9990
   chunk 17 optimal weight:    4.9990
   chunk 10 optimal weight:    0.2980
   chunk 27 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   overall best weight:    3.4588

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.129697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.114057 restraints weight = 3419.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 1.92
r_work: 0.3628 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3534 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8879
moved from start:          0.4073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   2915  Z= 0.207
  Angle     :  0.646   5.426   3900  Z= 0.327
  Chirality :  0.049   0.139    440
  Planarity :  0.004   0.068    495
  Dihedral  :  5.068  16.483    385
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 25.15 %
    Favored  : 73.33 %
  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: -1.92 (0.35), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.46 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG C 379 
 TYR   0.026   0.004   TYR E 310 
 PHE   0.018   0.003   PHE E 346 
 HIS   0.008   0.001   HIS A 330 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00496 /  0.21 ( 2915)
  covalent geometry    : angle       0.64557 /  0.33 ( 3900)
  hydrogen bonds       : bond        0.02033 /  1.32 (   58)
  hydrogen bonds       : angle       4.91829 /  3.30 (  174)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.103 
Fit side-chains
REVERT: A  338 GLU cc_start: 0.8489 (tt0) cc_final: 0.8094 (tm-30)
REVERT: A  349 ARG cc_start: 0.8502 (mtp180) cc_final: 0.8236 (mtp85)
REVERT: B  338 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8411 (tm-30)
REVERT: B  349 ARG cc_start: 0.8638 (mtt180) cc_final: 0.7110 (pmt-80)
REVERT: C  349 ARG cc_start: 0.8541 (mtt180) cc_final: 0.6832 (pmt-80)
REVERT: C  379 ARG cc_start: 0.8097 (ttm110) cc_final: 0.7408 (mtt180)
REVERT: D  321 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8393 (mtmt)
REVERT: D  338 GLU cc_start: 0.8512 (tt0) cc_final: 0.8143 (tm-30)
REVERT: D  349 ARG cc_start: 0.8375 (mtt180) cc_final: 0.7079 (mtt-85)
REVERT: D  379 ARG cc_start: 0.7567 (mmt180) cc_final: 0.6855 (mmt180)
REVERT: E  338 GLU cc_start: 0.8557 (tt0) cc_final: 0.8213 (tm-30)
REVERT: E  349 ARG cc_start: 0.8486 (mtt180) cc_final: 0.7030 (mmp-170)
  outliers start: 5
  outliers final: 4
  residues processed: 78
  average time/residue: 0.6717
  time to fit residues: 53.4798
Evaluate side-chains
  80 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  338 GLU
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain D residue  306 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   chunk 5 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 1 optimal weight:    9.9990
   chunk 31 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 15 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   overall best weight:    3.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.129006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.113602 restraints weight = 3374.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3739 rms_B_bonded: 1.89
r_work: 0.3623 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3529 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8880
moved from start:          0.4133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   2915  Z= 0.223
  Angle     :  0.671   5.265   3900  Z= 0.340
  Chirality :  0.050   0.141    440
  Planarity :  0.005   0.066    495
  Dihedral  :  5.161  16.846    385
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 25.15 %
    Favored  : 73.33 %
  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: -1.93 (0.35), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.46 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.002   ARG C 379 
 TYR   0.026   0.004   TYR E 310 
 PHE   0.019   0.004   PHE E 346 
 HIS   0.008   0.001   HIS A 330 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00536 /  0.22 ( 2915)
  covalent geometry    : angle       0.67092 /  0.34 ( 3900)
  hydrogen bonds       : bond        0.02090 /  1.35 (   58)
  hydrogen bonds       : angle       4.97907 /  3.34 (  174)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A  338 GLU cc_start: 0.8510 (tt0) cc_final: 0.8103 (tm-30)
REVERT: A  349 ARG cc_start: 0.8518 (mtp180) cc_final: 0.8248 (mtp85)
REVERT: B  338 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8415 (tm-30)
REVERT: B  349 ARG cc_start: 0.8639 (mtt180) cc_final: 0.7105 (pmt-80)
REVERT: B  379 ARG cc_start: 0.8187 (ttm110) cc_final: 0.7154 (mtt180)
REVERT: C  349 ARG cc_start: 0.8530 (mtt180) cc_final: 0.6831 (pmt-80)
REVERT: C  379 ARG cc_start: 0.8112 (ttm110) cc_final: 0.7408 (mtt180)
REVERT: D  321 LYS cc_start: 0.8689 (mtpt) cc_final: 0.8408 (mtmt)
REVERT: D  338 GLU cc_start: 0.8511 (tt0) cc_final: 0.8133 (tm-30)
REVERT: D  349 ARG cc_start: 0.8373 (mtt180) cc_final: 0.7072 (mtt-85)
REVERT: D  379 ARG cc_start: 0.7572 (mmt180) cc_final: 0.6869 (mmt180)
REVERT: E  338 GLU cc_start: 0.8553 (tt0) cc_final: 0.8203 (tm-30)
REVERT: E  349 ARG cc_start: 0.8481 (mtt180) cc_final: 0.7030 (mmp-170)
  outliers start: 5
  outliers final: 4
  residues processed: 78
  average time/residue: 0.6737
  time to fit residues: 53.5662
Evaluate side-chains
  80 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  338 GLU
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain D residue  306 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 17 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9990
   chunk 26 optimal weight:    0.3980
   chunk 13 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 16 optimal weight:    8.9990
   chunk 0 optimal weight:    8.9990
   chunk 2 optimal weight:    7.9990
   overall best weight:    2.4788

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.130998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.115792 restraints weight = 3338.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3769 rms_B_bonded: 1.89
r_work: 0.3654 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3560 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8861
moved from start:          0.4133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2915  Z= 0.158
  Angle     :  0.618   5.110   3900  Z= 0.310
  Chirality :  0.049   0.134    440
  Planarity :  0.004   0.064    495
  Dihedral  :  5.003  15.749    385
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 25.45 %
    Favored  : 73.33 %
  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: -1.90 (0.35), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.44 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.002   ARG C 379 
 TYR   0.025   0.004   TYR E 310 
 PHE   0.013   0.003   PHE B 346 
 HIS   0.006   0.001   HIS A 330 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00381 /  0.16 ( 2915)
  covalent geometry    : angle       0.61802 /  0.31 ( 3900)
  hydrogen bonds       : bond        0.01847 /  1.19 (   58)
  hydrogen bonds       : angle       4.89478 /  3.30 (  174)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1711.50 seconds
wall clock time: 30 minutes 1.07 seconds (1801.07 seconds total)