Starting phenix.real_space_refine
on Tue Mar  3 10:49:51 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ql1_14060/03_2026/7ql1_14060.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ql1_14060/03_2026/7ql1_14060.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.34
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ql1_14060/03_2026/7ql1_14060.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ql1_14060/03_2026/7ql1_14060.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ql1_14060/03_2026/7ql1_14060.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ql1_14060/03_2026/7ql1_14060.cif"
  }
  resolution = 3.34
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.006
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       3      5.16       5
     C    1053      2.51       5
     N     303      2.21       5
     O     312      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 1671
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 557
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "C"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 557
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "D"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 557
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
  Time building chain proxies: 0.65, per 1000 atoms: 0.39
  Number of scatterers: 1671
  At special positions: 0
  Unit cell: (78.516, 85.786, 39.258, 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       3     16.00
     O     312      8.00
     N     303      7.00
     C    1053      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: 0.07
  Conformation dependent library (CDL) restraints added in 92.1 milliseconds
  

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  384

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 9 sheets defined
      0.0% alpha, 35.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 307 through 310
    Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314
      removed outlier: 6.749A  pdb=" N   VAL C 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 318
      removed outlier: 6.543A  pdb=" N   LYS C 317 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 330
      removed outlier: 5.864A  pdb=" N   GLY A 326 " --> pdb=" O   ASN D 327 " (cutoff:3.500A)
      removed outlier: 8.477A  pdb=" N   HIS D 329 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   ILE A 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   GLY D 326 " --> pdb=" O   LEU C 325 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ASN C 327 " --> pdb=" O   GLY D 326 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 337 through 342
      removed outlier: 6.307A  pdb=" N   GLU C 338 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
      removed outlier: 8.110A  pdb=" N   SER D 341 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   LYS C 340 " --> pdb=" O   SER D 341 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 346
      removed outlier: 6.512A  pdb=" N   ASP C 345 " --> pdb=" O   PHE D 346 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 355
      removed outlier: 6.497A  pdb=" N   LYS C 353 " --> pdb=" O   ILE D 354 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 360 through 362
      removed outlier: 6.431A  pdb=" N   THR A 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 371 through 377
      removed outlier: 6.964A  pdb=" N   ILE C 371 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 8.396A  pdb=" N   HIS D 374 " --> pdb=" O   ILE C 371 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   THR C 373 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
      removed outlier: 8.071A  pdb=" N   LEU D 376 " --> pdb=" O   THR C 373 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   LYS C 375 " --> pdb=" O   LEU D 376 " (cutoff:3.500A)

    27 hydrogen bonds defined for protein.
    81 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: 0.25

  Time building geometry restraints manager: 0.12 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: 477
        1.33 -     1.45: 204
        1.45 -     1.57: 1014
        1.57 -     1.68: 0
        1.68 -     1.80: 3
  Bond restraints: 1698
  Sorted by residual:
  bond pdb=" CZ  ARG A 349 "
       pdb=" NH2 ARG A 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.75e+00
  bond pdb=" CB  THR C 361 "
       pdb=" OG1 THR C 361 "
    ideal  model  delta    sigma   weight residual
    1.433  1.389  0.044 1.60e-02 3.91e+03 7.42e+00
  bond pdb=" CB  THR A 361 "
       pdb=" OG1 THR A 361 "
    ideal  model  delta    sigma   weight residual
    1.433  1.391  0.042 1.60e-02 3.91e+03 7.01e+00
  bond pdb=" CZ  ARG C 349 "
       pdb=" NH2 ARG C 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.94e+00
  bond pdb=" CZ  ARG D 349 "
       pdb=" NH2 ARG D 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.81e+00
  ... (remaining 1693 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 1325
        1.50 -     2.99: 655
        2.99 -     4.49: 215
        4.49 -     5.98: 62
        5.98 -     7.48: 17
  Bond angle restraints: 2274
  Sorted by residual:
  angle pdb=" CA  ASP D 314 "
        pdb=" CB  ASP D 314 "
        pdb=" CG  ASP D 314 "
      ideal   model   delta    sigma   weight residual
     112.60  119.30   -6.70 1.00e+00 1.00e+00 4.49e+01
  angle pdb=" CA  ASP C 314 "
        pdb=" CB  ASP C 314 "
        pdb=" CG  ASP C 314 "
      ideal   model   delta    sigma   weight residual
     112.60  118.83   -6.23 1.00e+00 1.00e+00 3.88e+01
  angle pdb=" CB  HIS A 329 "
        pdb=" CG  HIS A 329 "
        pdb=" CD2 HIS A 329 "
      ideal   model   delta    sigma   weight residual
     131.20  124.98    6.22 1.30e+00 5.92e-01 2.29e+01
  angle pdb=" CB  HIS A 374 "
        pdb=" CG  HIS A 374 "
        pdb=" CD2 HIS A 374 "
      ideal   model   delta    sigma   weight residual
     131.20  125.03    6.17 1.30e+00 5.92e-01 2.25e+01
  angle pdb=" C   LYS C 311 "
        pdb=" CA  LYS C 311 "
        pdb=" CB  LYS C 311 "
      ideal   model   delta    sigma   weight residual
     111.11  117.00   -5.89 1.28e+00 6.10e-01 2.11e+01
  ... (remaining 2269 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.53: 798
        8.53 -    17.06: 162
       17.06 -    25.59: 42
       25.59 -    34.12: 21
       34.12 -    42.65: 9
  Dihedral angle restraints: 1032
    sinusoidal: 429
      harmonic: 603
  Sorted by residual:
  dihedral pdb=" CA  ASP C 314 "
           pdb=" C   ASP C 314 "
           pdb=" N   LEU C 315 "
           pdb=" CA  LEU C 315 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.10   28.90     0      5.00e+00 4.00e-02 3.34e+01
  dihedral pdb=" CA  GLY A 365 "
           pdb=" C   GLY A 365 "
           pdb=" N   GLY A 366 "
           pdb=" CA  GLY A 366 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.69   28.31     0      5.00e+00 4.00e-02 3.21e+01
  dihedral pdb=" CA  GLN C 336 "
           pdb=" C   GLN C 336 "
           pdb=" N   VAL C 337 "
           pdb=" CA  VAL C 337 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.75   28.25     0      5.00e+00 4.00e-02 3.19e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 96
       0.049 -    0.097: 67
       0.097 -    0.146: 50
       0.146 -    0.194: 30
       0.194 -    0.243: 15
  Chirality restraints: 258
  Sorted by residual:
  chirality pdb=" CA  LYS C 311 "
            pdb=" N   LYS C 311 "
            pdb=" C   LYS C 311 "
            pdb=" CB  LYS C 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.48e+00
  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    2.27    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CA  ILE C 328 "
            pdb=" N   ILE C 328 "
            pdb=" C   ILE C 328 "
            pdb=" CB  ILE C 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.44e+00
  ... (remaining 255 not shown)

  Planarity restraints: 288
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 310 "   -0.095 2.00e-02 2.50e+03   5.25e-02 5.51e+01
        pdb=" CG  TYR D 310 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 310 "    0.043 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 310 "    0.039 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 310 "    0.027 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 310 "    0.034 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 310 "    0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR D 310 "   -0.082 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 310 "   -0.073 2.00e-02 2.50e+03   4.12e-02 3.40e+01
        pdb=" CG  TYR C 310 "    0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 310 "    0.028 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 310 "    0.036 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 310 "    0.028 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 310 "    0.024 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 310 "    0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR C 310 "   -0.067 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 310 "   -0.058 2.00e-02 2.50e+03   2.98e-02 1.78e+01
        pdb=" CG  TYR A 310 "    0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 310 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 310 "    0.028 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 310 "    0.014 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 310 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 310 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 310 "   -0.039 2.00e-02 2.50e+03
  ... (remaining 285 not shown)

  Histogram of nonbonded interaction distances:
        2.65 -     3.10: 1125
        3.10 -     3.55: 1466
        3.55 -     4.00: 2463
        4.00 -     4.45: 2760
        4.45 -     4.90: 4982
  Nonbonded interactions: 12796
  Sorted by model distance:
  nonbonded pdb=" N   GLY A 366 "
            pdb=" O   GLY A 366 "
     model   vdw
     2.654 2.496
  nonbonded pdb=" O   LEU D 325 "
            pdb=" CA  GLY D 326 "
     model   vdw
     2.655 2.752
  nonbonded pdb=" N   GLY D 366 "
            pdb=" O   GLY D 366 "
     model   vdw
     2.656 2.496
  nonbonded pdb=" O   PRO C 332 "
            pdb=" OG  SER D 356 "
     model   vdw
     2.656 3.040
  nonbonded pdb=" NZ  LYS D 370 "
            pdb=" OE1 GLU D 372 "
     model   vdw
     2.663 3.120
  ... (remaining 12791 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 'D'
}

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:             0.280
  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:          0.030
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     3.670
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
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   0.044   1698  Z= 0.698
  Angle     :  2.010   7.476   2274  Z= 1.340
  Chirality :  0.103   0.243    258
  Planarity :  0.013   0.056    288
  Dihedral  : 11.062  42.647    648
  Min Nonbonded Distance : 2.654

Molprobity Statistics.
  All-atom Clashscore : 0.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.09 (0.42), residues: 213
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.35 (0.32), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 349 
 TYR   0.095   0.035   TYR D 310 
 PHE   0.031   0.012   PHE A 378 
 HIS   0.010   0.003   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.01078 ( 1698)
  covalent geometry    : angle       2.01023 ( 2274)
  hydrogen bonds       : bond        0.08736 (   27)
  hydrogen bonds       : angle       6.90379 (   81)

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

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

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.042 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.8985 (mttt) cc_final: 0.8328 (pttm)
REVERT: A  348 ASP cc_start: 0.8712 (t0) cc_final: 0.7898 (p0)
REVERT: A  356 SER cc_start: 0.8863 (p) cc_final: 0.8517 (p)
REVERT: C  349 ARG cc_start: 0.8785 (mtt180) cc_final: 0.7848 (mmp-170)
REVERT: C  370 LYS cc_start: 0.8476 (tttt) cc_final: 0.8120 (tttt)
REVERT: D  321 LYS cc_start: 0.8435 (mttt) cc_final: 0.8173 (mtpt)
REVERT: D  347 LYS cc_start: 0.9016 (mttt) cc_final: 0.8763 (mptt)
REVERT: D  370 LYS cc_start: 0.8664 (tttt) cc_final: 0.8380 (tttm)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.1202
  time to fit residues: 11.3305
Evaluate side-chains
  74 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 13 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 362 HIS
C 362 HIS
** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 362 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.132227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.115544 restraints weight = 2478.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3933 rms_B_bonded: 2.65
r_work: 0.3806 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.3499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   1698  Z= 0.137
  Angle     :  0.725   6.309   2274  Z= 0.369
  Chirality :  0.052   0.143    258
  Planarity :  0.004   0.033    288
  Dihedral  :  7.095  25.386    222
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 16.67 %
    Favored  : 81.77 %
  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: -2.20 (0.43), residues: 213
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.67 (0.33), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 349 
 TYR   0.007   0.001   TYR D 310 
 PHE   0.007   0.002   PHE D 346 
 HIS   0.008   0.002   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 1698)
  covalent geometry    : angle       0.72495 ( 2274)
  hydrogen bonds       : bond        0.01901 (   27)
  hydrogen bonds       : angle       5.51893 (   81)

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

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

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 74
  time to evaluate  : 0.067 
Fit side-chains
   revert: symmetry clash
REVERT: A  336 GLN cc_start: 0.8230 (mp10) cc_final: 0.8017 (mp10)
REVERT: A  347 LYS cc_start: 0.8985 (mttt) cc_final: 0.8076 (pttm)
REVERT: A  348 ASP cc_start: 0.8615 (t0) cc_final: 0.6517 (p0)
REVERT: A  356 SER cc_start: 0.8732 (p) cc_final: 0.8146 (p)
REVERT: A  370 LYS cc_start: 0.8871 (ttmt) cc_final: 0.8650 (tttt)
REVERT: C  311 LYS cc_start: 0.8701 (ttmt) cc_final: 0.7532 (mmtm)
REVERT: C  336 GLN cc_start: 0.8580 (mp10) cc_final: 0.7719 (mp10)
REVERT: C  348 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.7889 (t70)
REVERT: C  349 ARG cc_start: 0.7932 (mtt180) cc_final: 0.6699 (mmp-170)
REVERT: C  377 THR cc_start: 0.8135 (t) cc_final: 0.7914 (p)
REVERT: D  321 LYS cc_start: 0.8025 (mttt) cc_final: 0.7644 (mtpt)
REVERT: D  340 LYS cc_start: 0.8583 (mtpp) cc_final: 0.8132 (mppt)
REVERT: D  342 GLU cc_start: 0.8205 (mp0) cc_final: 0.7818 (mp0)
REVERT: D  347 LYS cc_start: 0.8825 (mttt) cc_final: 0.8374 (mppt)
REVERT: D  349 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7351 (mtp85)
  outliers start: 3
  outliers final: 0
  residues processed: 75
  average time/residue: 0.1019
  time to fit residues: 8.2255
Evaluate side-chains
  57 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  348 ASP
Chi-restraints excluded: chain D residue  349 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 17 optimal weight:   10.0000
   chunk 20 optimal weight:    8.9990
   chunk 12 optimal weight:    0.4980
   chunk 5 optimal weight:    7.9990
   chunk 11 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 8 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
C 359 ASN
** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 359 ASN
D 362 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.128637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.112487 restraints weight = 2463.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3913 rms_B_bonded: 2.59
r_work: 0.3822 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3715 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.3942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   1698  Z= 0.158
  Angle     :  0.669   5.862   2274  Z= 0.336
  Chirality :  0.051   0.142    258
  Planarity :  0.004   0.032    288
  Dihedral  :  6.237  20.454    222
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 17.71 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.16 (0.42), residues: 213
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.64 (0.32), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 349 
 TYR   0.012   0.002   TYR D 310 
 PHE   0.005   0.001   PHE D 346 
 HIS   0.008   0.002   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 1698)
  covalent geometry    : angle       0.66875 ( 2274)
  hydrogen bonds       : bond        0.01568 (   27)
  hydrogen bonds       : angle       4.92420 (   81)

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

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

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 58
  time to evaluate  : 0.071 
Fit side-chains
REVERT: A  336 GLN cc_start: 0.8377 (mp10) cc_final: 0.7970 (mp10)
REVERT: A  347 LYS cc_start: 0.9060 (mttt) cc_final: 0.7990 (pttm)
REVERT: A  348 ASP cc_start: 0.8658 (t0) cc_final: 0.6007 (p0)
REVERT: A  368 ASN cc_start: 0.8867 (m110) cc_final: 0.8632 (m110)
REVERT: C  311 LYS cc_start: 0.8780 (ttmt) cc_final: 0.7619 (mmtm)
REVERT: C  336 GLN cc_start: 0.8157 (mp10) cc_final: 0.6847 (mm110)
REVERT: C  349 ARG cc_start: 0.7973 (mtt180) cc_final: 0.6494 (mmp-170)
REVERT: C  370 LYS cc_start: 0.8473 (tttm) cc_final: 0.8195 (tptp)
REVERT: C  371 ILE cc_start: 0.8747 (mm) cc_final: 0.8531 (mt)
REVERT: C  377 THR cc_start: 0.8094 (t) cc_final: 0.7864 (p)
REVERT: C  378 PHE cc_start: 0.7139 (m-80) cc_final: 0.6713 (m-80)
REVERT: D  349 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7511 (mtp85)
  outliers start: 2
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0811
  time to fit residues: 5.2819
Evaluate side-chains
  59 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  349 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 11 optimal weight:    5.9990
   chunk 7 optimal weight:    8.9990
   chunk 2 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   chunk 16 optimal weight:    7.9990
   chunk 0 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 10 optimal weight:    9.9990
   chunk 19 optimal weight:    0.0970
   chunk 3 optimal weight:    7.9990
   overall best weight:    5.2186

-------------------------------------------------------------------------------
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**
** D 327 ASN ** 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 = 0.3985 r_free = 0.3985 target = 0.119735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.103697 restraints weight = 2607.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3788 rms_B_bonded: 2.57
r_work: 0.3681 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3569 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.4099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.058   1698  Z= 0.373
  Angle     :  0.784   6.247   2274  Z= 0.404
  Chirality :  0.057   0.151    258
  Planarity :  0.004   0.041    288
  Dihedral  :  6.831  20.793    222
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 18.23 %
    Favored  : 79.17 %
  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: -2.49 (0.41), residues: 213
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.89 (0.31), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG D 349 
 TYR   0.019   0.004   TYR D 310 
 PHE   0.010   0.002   PHE C 378 
 HIS   0.008   0.002   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00843 ( 1698)
  covalent geometry    : angle       0.78351 ( 2274)
  hydrogen bonds       : bond        0.02282 (   27)
  hydrogen bonds       : angle       4.65470 (   81)

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

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

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.068 
Fit side-chains
REVERT: A  336 GLN cc_start: 0.8482 (mp10) cc_final: 0.8100 (mp10)
REVERT: A  348 ASP cc_start: 0.8567 (t0) cc_final: 0.7112 (p0)
REVERT: A  356 SER cc_start: 0.8433 (p) cc_final: 0.7692 (p)
REVERT: C  336 GLN cc_start: 0.8500 (mp10) cc_final: 0.8100 (mp10)
REVERT: C  349 ARG cc_start: 0.8203 (mtt180) cc_final: 0.6611 (mmm160)
REVERT: C  377 THR cc_start: 0.8262 (t) cc_final: 0.7942 (p)
REVERT: D  349 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7714 (mtp85)
REVERT: D  368 ASN cc_start: 0.9223 (m-40) cc_final: 0.8789 (m-40)
  outliers start: 5
  outliers final: 4
  residues processed: 56
  average time/residue: 0.0665
  time to fit residues: 4.1590
Evaluate side-chains
  62 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain D residue  349 ARG
Chi-restraints excluded: chain D residue  375 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 12 optimal weight:    0.4980
   chunk 4 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0070
   chunk 13 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    1.5004

-------------------------------------------------------------------------------
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**
** D 327 ASN ** 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 = 0.4088 r_free = 0.4088 target = 0.127446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.111372 restraints weight = 2518.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3898 rms_B_bonded: 2.64
r_work: 0.3801 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3692 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.4502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   1698  Z= 0.139
  Angle     :  0.623   5.546   2274  Z= 0.315
  Chirality :  0.051   0.132    258
  Planarity :  0.003   0.039    288
  Dihedral  :  5.948  17.425    222
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 19.27 %
    Favored  : 78.65 %
  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: -2.36 (0.43), residues: 213
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.79 (0.33), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG D 349 
 TYR   0.015   0.002   TYR D 310 
 PHE   0.004   0.001   PHE D 346 
 HIS   0.006   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 1698)
  covalent geometry    : angle       0.62286 ( 2274)
  hydrogen bonds       : bond        0.01385 (   27)
  hydrogen bonds       : angle       4.51870 (   81)

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

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

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.071 
Fit side-chains
REVERT: A  336 GLN cc_start: 0.8295 (mp10) cc_final: 0.8032 (mp10)
REVERT: A  347 LYS cc_start: 0.8975 (mttt) cc_final: 0.8193 (pttm)
REVERT: A  348 ASP cc_start: 0.8633 (t0) cc_final: 0.6807 (p0)
REVERT: A  353 LYS cc_start: 0.8921 (mttt) cc_final: 0.8711 (mtpt)
REVERT: A  356 SER cc_start: 0.8413 (p) cc_final: 0.7674 (p)
REVERT: C  311 LYS cc_start: 0.8778 (ttmt) cc_final: 0.7550 (mmtm)
REVERT: C  336 GLN cc_start: 0.8370 (mp10) cc_final: 0.6977 (mm110)
REVERT: C  348 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7723 (t70)
REVERT: C  349 ARG cc_start: 0.8135 (mtt180) cc_final: 0.6508 (mmp-170)
REVERT: C  378 PHE cc_start: 0.7104 (m-80) cc_final: 0.6864 (m-80)
REVERT: D  336 GLN cc_start: 0.8659 (mp10) cc_final: 0.8416 (mp10)
REVERT: D  349 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7549 (mtp85)
  outliers start: 4
  outliers final: 2
  residues processed: 63
  average time/residue: 0.0670
  time to fit residues: 4.6922
Evaluate side-chains
  60 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain C residue  348 ASP
Chi-restraints excluded: chain D residue  349 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 3 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   chunk 6 optimal weight:    8.9990
   chunk 9 optimal weight:   10.0000
   chunk 0 optimal weight:    0.6980
   chunk 2 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    3.7186

-------------------------------------------------------------------------------
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**
** D 327 ASN ** 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 = 0.4000 r_free = 0.4000 target = 0.120681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.104441 restraints weight = 2546.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3798 rms_B_bonded: 2.59
r_work: 0.3695 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3585 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.4515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   1698  Z= 0.270
  Angle     :  0.696   5.054   2274  Z= 0.357
  Chirality :  0.053   0.135    258
  Planarity :  0.004   0.038    288
  Dihedral  :  6.206  18.281    222
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 19.27 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.43 (0.43), residues: 213
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.33), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG D 349 
 TYR   0.015   0.003   TYR D 310 
 PHE   0.008   0.002   PHE C 378 
 HIS   0.006   0.002   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00601 ( 1698)
  covalent geometry    : angle       0.69624 ( 2274)
  hydrogen bonds       : bond        0.01764 (   27)
  hydrogen bonds       : angle       4.35222 (   81)

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

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

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.076 
Fit side-chains
REVERT: A  336 GLN cc_start: 0.8396 (mp10) cc_final: 0.8118 (mp10)
REVERT: A  343 LYS cc_start: 0.8691 (mtpp) cc_final: 0.8421 (mtpp)
REVERT: A  347 LYS cc_start: 0.8986 (mttt) cc_final: 0.8205 (pttm)
REVERT: A  348 ASP cc_start: 0.8588 (t0) cc_final: 0.7101 (p0)
REVERT: A  353 LYS cc_start: 0.8910 (mttt) cc_final: 0.8702 (mtpt)
REVERT: C  336 GLN cc_start: 0.8595 (mp10) cc_final: 0.8131 (mp10)
REVERT: C  349 ARG cc_start: 0.8166 (mtt180) cc_final: 0.6585 (mmp-170)
REVERT: D  336 GLN cc_start: 0.8647 (mp10) cc_final: 0.8377 (mp10)
REVERT: D  349 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7394 (mtp85)
REVERT: D  368 ASN cc_start: 0.9236 (m-40) cc_final: 0.8767 (m-40)
  outliers start: 5
  outliers final: 4
  residues processed: 59
  average time/residue: 0.0798
  time to fit residues: 5.1121
Evaluate side-chains
  61 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain C residue  377 THR
Chi-restraints excluded: chain D residue  349 ARG
Chi-restraints excluded: chain D residue  375 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 2 optimal weight:    0.0980
   chunk 1 optimal weight:    6.9990
   chunk 10 optimal weight:    8.9990
   chunk 18 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 9 optimal weight:    8.9990
   chunk 8 optimal weight:    0.0870
   chunk 19 optimal weight:    0.9980
   chunk 7 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** D 327 ASN ** 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 = 0.4163 r_free = 0.4163 target = 0.132426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.116207 restraints weight = 2488.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 2.67
r_work: 0.3878 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3774 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.4936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   1698  Z= 0.097
  Angle     :  0.597   4.873   2274  Z= 0.304
  Chirality :  0.050   0.127    258
  Planarity :  0.004   0.037    288
  Dihedral  :  5.513  15.110    222
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 20.31 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.35 (0.44), residues: 213
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.34), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 349 
 TYR   0.014   0.003   TYR A 310 
 PHE   0.004   0.001   PHE D 346 
 HIS   0.004   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 1698)
  covalent geometry    : angle       0.59665 ( 2274)
  hydrogen bonds       : bond        0.01298 (   27)
  hydrogen bonds       : angle       4.41802 (   81)

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

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

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 57
  time to evaluate  : 0.064 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.9012 (mttt) cc_final: 0.8175 (pttm)
REVERT: A  348 ASP cc_start: 0.8610 (t0) cc_final: 0.6801 (p0)
REVERT: A  353 LYS cc_start: 0.8752 (mttt) cc_final: 0.8537 (mtpt)
REVERT: A  359 ASN cc_start: 0.9003 (m110) cc_final: 0.8043 (m110)
REVERT: C  311 LYS cc_start: 0.8669 (ttmt) cc_final: 0.7422 (mmtm)
REVERT: C  336 GLN cc_start: 0.8449 (mp10) cc_final: 0.7079 (mm110)
REVERT: C  348 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7646 (t70)
REVERT: C  349 ARG cc_start: 0.8121 (mtt180) cc_final: 0.6312 (mmm160)
REVERT: D  336 GLN cc_start: 0.8552 (mp10) cc_final: 0.8161 (mp10)
REVERT: D  338 GLU cc_start: 0.7850 (mp0) cc_final: 0.7376 (mp0)
REVERT: D  349 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7470 (mtp85)
  outliers start: 3
  outliers final: 1
  residues processed: 59
  average time/residue: 0.0773
  time to fit residues: 5.0200
Evaluate side-chains
  58 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain C residue  348 ASP
Chi-restraints excluded: chain D residue  349 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 5 optimal weight:    0.5980
   chunk 14 optimal weight:    0.5980
   chunk 9 optimal weight:    8.9990
   chunk 19 optimal weight:    1.9990
   chunk 15 optimal weight:    7.9990
   chunk 20 optimal weight:    7.9990
   chunk 10 optimal weight:   10.0000
   chunk 3 optimal weight:    9.9990
   chunk 1 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   overall best weight:    2.6386

-------------------------------------------------------------------------------
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**
** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 368 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.124333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.107857 restraints weight = 2576.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3841 rms_B_bonded: 2.63
r_work: 0.3744 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3637 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.4883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   1698  Z= 0.201
  Angle     :  0.644   4.800   2274  Z= 0.329
  Chirality :  0.051   0.129    258
  Planarity :  0.004   0.041    288
  Dihedral  :  5.617  16.000    222
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 20.83 %
    Favored  : 77.60 %
  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: -2.44 (0.45), residues: 213
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.34), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG D 349 
 TYR   0.014   0.003   TYR D 310 
 PHE   0.004   0.001   PHE D 346 
 HIS   0.005   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 1698)
  covalent geometry    : angle       0.64374 ( 2274)
  hydrogen bonds       : bond        0.01578 (   27)
  hydrogen bonds       : angle       4.17186 (   81)

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

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

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.066 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.8991 (mttt) cc_final: 0.8061 (pttm)
REVERT: A  348 ASP cc_start: 0.8614 (t0) cc_final: 0.6834 (p0)
REVERT: A  353 LYS cc_start: 0.8819 (mttt) cc_final: 0.8607 (mtpt)
REVERT: A  359 ASN cc_start: 0.8942 (m110) cc_final: 0.7923 (m110)
REVERT: C  311 LYS cc_start: 0.8800 (ttmt) cc_final: 0.7557 (mmtm)
REVERT: C  336 GLN cc_start: 0.8585 (mp10) cc_final: 0.7092 (mm110)
REVERT: C  349 ARG cc_start: 0.8152 (mtt180) cc_final: 0.6540 (mmp-170)
REVERT: D  336 GLN cc_start: 0.8707 (mp10) cc_final: 0.8389 (mp10)
REVERT: D  338 GLU cc_start: 0.7885 (mp0) cc_final: 0.7351 (mp0)
REVERT: D  349 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7775 (mtp85)
REVERT: D  368 ASN cc_start: 0.9249 (m-40) cc_final: 0.8781 (m110)
  outliers start: 3
  outliers final: 2
  residues processed: 58
  average time/residue: 0.0912
  time to fit residues: 5.7868
Evaluate side-chains
  59 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain C residue  377 THR
Chi-restraints excluded: chain D residue  349 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 14 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 6 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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**
** D 327 ASN ** 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 = 0.4046 r_free = 0.4046 target = 0.123871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.107293 restraints weight = 2534.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3846 rms_B_bonded: 2.62
r_work: 0.3746 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3635 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.4934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   1698  Z= 0.199
  Angle     :  0.663   5.195   2274  Z= 0.337
  Chirality :  0.052   0.128    258
  Planarity :  0.004   0.047    288
  Dihedral  :  5.703  16.302    222
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 21.35 %
    Favored  : 76.04 %
  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: -2.56 (0.44), residues: 213
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.94 (0.34), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG D 349 
 TYR   0.014   0.003   TYR D 310 
 PHE   0.005   0.001   PHE D 346 
 HIS   0.005   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 1698)
  covalent geometry    : angle       0.66293 ( 2274)
  hydrogen bonds       : bond        0.01545 (   27)
  hydrogen bonds       : angle       4.13545 (   81)

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

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

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.073 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.9025 (mttt) cc_final: 0.8049 (pttm)
REVERT: A  348 ASP cc_start: 0.8633 (t0) cc_final: 0.6840 (p0)
REVERT: A  353 LYS cc_start: 0.8837 (mttt) cc_final: 0.8618 (mtpt)
REVERT: A  359 ASN cc_start: 0.8829 (m110) cc_final: 0.7728 (m110)
REVERT: C  336 GLN cc_start: 0.8682 (mp10) cc_final: 0.7243 (mm110)
REVERT: C  348 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7907 (t70)
REVERT: C  349 ARG cc_start: 0.8159 (mtt180) cc_final: 0.6676 (mmp-170)
REVERT: D  336 GLN cc_start: 0.8702 (mp10) cc_final: 0.8411 (mp10)
REVERT: D  338 GLU cc_start: 0.7916 (mp0) cc_final: 0.7358 (mp0)
REVERT: D  342 GLU cc_start: 0.7899 (mp0) cc_final: 0.7678 (mp0)
REVERT: D  349 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7639 (mtp85)
REVERT: D  368 ASN cc_start: 0.9221 (m-40) cc_final: 0.8723 (m110)
  outliers start: 5
  outliers final: 3
  residues processed: 59
  average time/residue: 0.0812
  time to fit residues: 5.3034
Evaluate side-chains
  60 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain C residue  348 ASP
Chi-restraints excluded: chain C residue  377 THR
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain D residue  349 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 18 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   chunk 1 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 16 optimal weight:    8.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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**
** D 327 ASN ** 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 = 0.4045 r_free = 0.4045 target = 0.123904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.107427 restraints weight = 2502.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 2.59
r_work: 0.3749 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3639 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.4947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   1698  Z= 0.200
  Angle     :  0.666   5.747   2274  Z= 0.337
  Chirality :  0.052   0.130    258
  Planarity :  0.005   0.051    288
  Dihedral  :  5.703  16.388    222
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 21.88 %
    Favored  : 76.04 %
  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: -2.58 (0.44), residues: 213
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.96 (0.34), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG D 349 
 TYR   0.014   0.003   TYR D 310 
 PHE   0.005   0.001   PHE D 346 
 HIS   0.005   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 1698)
  covalent geometry    : angle       0.66575 ( 2274)
  hydrogen bonds       : bond        0.01556 (   27)
  hydrogen bonds       : angle       4.12466 (   81)

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

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

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.080 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8653 (mtpp) cc_final: 0.8351 (mtpp)
REVERT: A  347 LYS cc_start: 0.9028 (mttt) cc_final: 0.8056 (pttm)
REVERT: A  348 ASP cc_start: 0.8632 (t0) cc_final: 0.6881 (p0)
REVERT: A  353 LYS cc_start: 0.8830 (mttt) cc_final: 0.8611 (mtpt)
REVERT: A  359 ASN cc_start: 0.8842 (m110) cc_final: 0.7737 (m110)
REVERT: C  336 GLN cc_start: 0.8719 (mp10) cc_final: 0.7324 (mm110)
REVERT: C  348 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7985 (t70)
REVERT: C  349 ARG cc_start: 0.8182 (mtt180) cc_final: 0.6685 (mmp-170)
REVERT: D  336 GLN cc_start: 0.8716 (mp10) cc_final: 0.8426 (mp10)
REVERT: D  338 GLU cc_start: 0.7919 (mp0) cc_final: 0.7391 (mp0)
REVERT: D  342 GLU cc_start: 0.7899 (mp0) cc_final: 0.7674 (mp0)
REVERT: D  348 ASP cc_start: 0.8170 (t0) cc_final: 0.7913 (t0)
REVERT: D  349 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7650 (mtp85)
  outliers start: 4
  outliers final: 2
  residues processed: 59
  average time/residue: 0.0858
  time to fit residues: 5.5517
Evaluate side-chains
  60 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain C residue  348 ASP
Chi-restraints excluded: chain C residue  377 THR
Chi-restraints excluded: chain D residue  349 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 1 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 17 optimal weight:    8.9990
   chunk 6 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    2.1786

-------------------------------------------------------------------------------
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**
** D 327 ASN ** 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 = 0.4048 r_free = 0.4048 target = 0.124678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.108184 restraints weight = 2500.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 2.61
r_work: 0.3753 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3643 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.5013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   1698  Z= 0.174
  Angle     :  0.652   5.973   2274  Z= 0.329
  Chirality :  0.051   0.127    258
  Planarity :  0.004   0.051    288
  Dihedral  :  5.609  16.008    222
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 23.44 %
    Favored  : 74.48 %
  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: -2.60 (0.44), residues: 213
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.34), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG D 349 
 TYR   0.014   0.003   TYR D 310 
 PHE   0.005   0.001   PHE D 346 
 HIS   0.005   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 1698)
  covalent geometry    : angle       0.65216 ( 2274)
  hydrogen bonds       : bond        0.01533 (   27)
  hydrogen bonds       : angle       4.11994 (   81)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 666.89 seconds
wall clock time: 12 minutes 19.68 seconds (739.68 seconds total)