Starting phenix.real_space_refine
on Wed Sep 17 02:57:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qjh_4563/09_2025/6qjh_4563.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qjh_4563/09_2025/6qjh_4563.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qjh_4563/09_2025/6qjh_4563.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qjh_4563/09_2025/6qjh_4563.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qjh_4563/09_2025/6qjh_4563.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qjh_4563/09_2025/6qjh_4563.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C     810      2.51       5
     N     243      2.21       5
     O     243      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 1302
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 434
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 434
          Classifications: {'peptide': 59}
          Link IDs: {'PTRANS': 2, 'TRANS': 56}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 0.28, per 1000 atoms: 0.22
  Number of scatterers: 1302
  At special positions: 0
  Unit cell: (59.34, 99.36, 49.68, 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       6     16.00
     O     243      8.00
     N     243      7.00
     C     810      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: 0.25
  Conformation dependent library (CDL) restraints added in 45.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  342 Ramachandran restraints generated.
    171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  306

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 44.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.03
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 275 through 291
      removed outlier: 6.188A  pdb=" N   VAL A 275 " --> pdb=" O   GLN C 276 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   ILE C 278 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   ILE A 277 " --> pdb=" O   ILE C 278 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   LYS C 280 " --> pdb=" O   ILE A 277 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   ASN A 279 " --> pdb=" O   LYS C 280 " (cutoff:3.500A)
      removed outlier: 7.741A  pdb=" N   LEU C 282 " --> pdb=" O   ASN A 279 " (cutoff:3.500A)
      removed outlier: 8.451A  pdb=" N   LYS A 281 " --> pdb=" O   LEU C 282 " (cutoff:3.500A)
      removed outlier: 9.701A  pdb=" N   LEU C 284 " --> pdb=" O   LYS A 281 " (cutoff:3.500A)
      removed outlier: 9.058A  pdb=" N   ASP A 283 " --> pdb=" O   LEU C 284 " (cutoff:3.500A)
      removed outlier: 9.960A  pdb=" N   ASN C 286 " --> pdb=" O   ASP A 283 " (cutoff:3.500A)
      removed outlier: 9.027A  pdb=" N   SER A 285 " --> pdb=" O   ASN C 286 " (cutoff:3.500A)
      removed outlier: 10.074A  pdb=" N   GLN C 288 " --> pdb=" O   SER A 285 " (cutoff:3.500A)
      removed outlier: 8.824A  pdb=" N   VAL A 287 " --> pdb=" O   GLN C 288 " (cutoff:3.500A)
      removed outlier: 10.302A  pdb=" N   LYS C 290 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 8.964A  pdb=" N   SER A 289 " --> pdb=" O   LYS C 290 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   LEU A 282 " --> pdb=" O   LYS B 281 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   ASP B 283 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   LEU A 284 " --> pdb=" O   ASP B 283 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   SER B 285 " --> pdb=" O   LEU A 284 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   ASN A 286 " --> pdb=" O   SER B 285 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   VAL B 287 " --> pdb=" O   ASN A 286 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   GLN A 288 " --> pdb=" O   VAL B 287 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   SER B 289 " --> pdb=" O   GLN A 288 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   LYS A 290 " --> pdb=" O   SER B 289 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   CYS B 291 " --> pdb=" O   LYS A 290 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 296 through 298
      removed outlier: 6.359A  pdb=" N   ASN A 296 " --> pdb=" O   ILE B 297 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 305 through 310
      removed outlier: 6.693A  pdb=" N   SER A 305 " --> pdb=" O   VAL C 306 " (cutoff:3.500A)
      removed outlier: 8.306A  pdb=" N   ILE C 308 " --> pdb=" O   SER A 305 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   GLN A 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   TYR C 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   VAL A 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 313 through 314
      removed outlier: 7.051A  pdb=" N   VAL A 313 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 317 through 318
      removed outlier: 6.614A  pdb=" N   LYS A 317 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 328
      removed outlier: 6.513A  pdb=" N   ASN A 327 " --> pdb=" O   ILE C 328 " (cutoff:3.500A)

    16 hydrogen bonds defined for protein.
    48 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: 0.08

  Time building geometry restraints manager: 0.25 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 321
        1.34 -     1.46: 261
        1.46 -     1.58: 729
        1.58 -     1.70: 0
        1.70 -     1.82: 6
  Bond restraints: 1317
  Sorted by residual:
  bond pdb=" C   LYS C 311 "
       pdb=" N   PRO C 312 "
    ideal  model  delta    sigma   weight residual
    1.334  1.379 -0.045 1.11e-02 8.12e+03 1.65e+01
  bond pdb=" C   LYS A 311 "
       pdb=" N   PRO A 312 "
    ideal  model  delta    sigma   weight residual
    1.334  1.379 -0.045 1.11e-02 8.12e+03 1.65e+01
  bond pdb=" C   LYS B 311 "
       pdb=" N   PRO B 312 "
    ideal  model  delta    sigma   weight residual
    1.334  1.379 -0.045 1.11e-02 8.12e+03 1.62e+01
  bond pdb=" C   VAL B 300 "
       pdb=" N   PRO B 301 "
    ideal  model  delta    sigma   weight residual
    1.329  1.372 -0.043 1.25e-02 6.40e+03 1.19e+01
  bond pdb=" C   VAL A 300 "
       pdb=" N   PRO A 301 "
    ideal  model  delta    sigma   weight residual
    1.329  1.372 -0.042 1.25e-02 6.40e+03 1.15e+01
  ... (remaining 1312 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.34: 1401
        1.34 -     2.68: 282
        2.68 -     4.02: 69
        4.02 -     5.36: 6
        5.36 -     6.70: 3
  Bond angle restraints: 1761
  Sorted by residual:
  angle pdb=" CA  LYS A 311 "
        pdb=" C   LYS A 311 "
        pdb=" N   PRO A 312 "
      ideal   model   delta    sigma   weight residual
     118.16  121.34   -3.18 7.00e-01 2.04e+00 2.07e+01
  angle pdb=" CA  LYS C 311 "
        pdb=" C   LYS C 311 "
        pdb=" N   PRO C 312 "
      ideal   model   delta    sigma   weight residual
     118.16  121.31   -3.15 7.00e-01 2.04e+00 2.02e+01
  angle pdb=" CA  LYS B 311 "
        pdb=" C   LYS B 311 "
        pdb=" N   PRO B 312 "
      ideal   model   delta    sigma   weight residual
     118.16  121.30   -3.14 7.00e-01 2.04e+00 2.01e+01
  angle pdb=" C   TYR B 310 "
        pdb=" N   LYS B 311 "
        pdb=" CA  LYS B 311 "
      ideal   model   delta    sigma   weight residual
     123.10  126.35   -3.25 9.60e-01 1.09e+00 1.14e+01
  angle pdb=" C   LYS B 281 "
        pdb=" CA  LYS B 281 "
        pdb=" CB  LYS B 281 "
      ideal   model   delta    sigma   weight residual
     110.42  117.12   -6.70 1.99e+00 2.53e-01 1.13e+01
  ... (remaining 1756 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.02 -    10.52: 630
       10.52 -    21.02: 126
       21.02 -    31.52: 24
       31.52 -    42.01: 12
       42.01 -    52.51: 15
  Dihedral angle restraints: 807
    sinusoidal: 324
      harmonic: 483
  Sorted by residual:
  dihedral pdb=" C   LYS B 281 "
           pdb=" N   LYS B 281 "
           pdb=" CA  LYS B 281 "
           pdb=" CB  LYS B 281 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.03   10.43     0      2.50e+00 1.60e-01 1.74e+01
  dihedral pdb=" C   LYS A 281 "
           pdb=" N   LYS A 281 "
           pdb=" CA  LYS A 281 "
           pdb=" CB  LYS A 281 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.01   10.41     0      2.50e+00 1.60e-01 1.73e+01
  dihedral pdb=" C   LYS C 281 "
           pdb=" N   LYS C 281 "
           pdb=" CA  LYS C 281 "
           pdb=" CB  LYS C 281 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.99   10.39     0      2.50e+00 1.60e-01 1.73e+01
  ... (remaining 804 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 126
       0.077 -    0.153: 67
       0.153 -    0.229: 8
       0.229 -    0.305: 0
       0.305 -    0.381: 3
  Chirality restraints: 204
  Sorted by residual:
  chirality pdb=" CA  LYS A 281 "
            pdb=" N   LYS A 281 "
            pdb=" C   LYS A 281 "
            pdb=" CB  LYS A 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.62e+00
  chirality pdb=" CA  LYS B 281 "
            pdb=" N   LYS B 281 "
            pdb=" C   LYS B 281 "
            pdb=" CB  LYS B 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.62e+00
  chirality pdb=" CA  LYS C 281 "
            pdb=" N   LYS C 281 "
            pdb=" C   LYS C 281 "
            pdb=" CB  LYS C 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.58e+00
  ... (remaining 201 not shown)

  Planarity restraints: 222
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 321 "   -0.013 2.00e-02 2.50e+03   2.64e-02 6.96e+00
        pdb=" C   LYS A 321 "    0.046 2.00e-02 2.50e+03
        pdb=" O   LYS A 321 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   CYS A 322 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 321 "   -0.013 2.00e-02 2.50e+03   2.63e-02 6.93e+00
        pdb=" C   LYS B 321 "    0.046 2.00e-02 2.50e+03
        pdb=" O   LYS B 321 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   CYS B 322 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 321 "   -0.013 2.00e-02 2.50e+03   2.63e-02 6.92e+00
        pdb=" C   LYS C 321 "    0.045 2.00e-02 2.50e+03
        pdb=" O   LYS C 321 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   CYS C 322 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 219 not shown)

  Histogram of nonbonded interaction distances:
        2.67 -     3.12: 828
        3.12 -     3.56: 1250
        3.56 -     4.01: 1878
        4.01 -     4.45: 1792
        4.45 -     4.90: 3861
  Nonbonded interactions: 9609
  Sorted by model distance:
  nonbonded pdb=" N   LEU C 325 "
            pdb=" O   LEU C 325 "
     model   vdw
     2.674 2.496
  nonbonded pdb=" N   LEU A 325 "
            pdb=" O   LEU A 325 "
     model   vdw
     2.674 2.496
  nonbonded pdb=" N   LEU B 325 "
            pdb=" O   LEU B 325 "
     model   vdw
     2.674 2.496
  nonbonded pdb=" O   VAL A 275 "
            pdb=" N   GLN C 276 "
     model   vdw
     2.676 3.120
  nonbonded pdb=" N   LYS A 311 "
            pdb=" O   TYR C 310 "
     model   vdw
     2.682 3.120
  ... (remaining 9604 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 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.000
  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:             0.010
  Extract box with map and model:          0.020
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     2.390
  Find NCS groups from input model:        0.010
  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:0.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    4.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
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      :  0.012   0.054   1317  Z= 0.791
  Angle     :  1.206   6.702   1761  Z= 0.777
  Chirality :  0.096   0.381    204
  Planarity :  0.010   0.039    222
  Dihedral  : 14.394  52.512    501
  Min Nonbonded Distance : 2.674

Molprobity Statistics.
  All-atom Clashscore : 1.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 11.76 %
    Favored  : 86.27 %
  Cbeta Deviations :  1.96 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.22 (0.46), residues: 171
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.45 (0.35), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.011   0.004   TYR A 310 
 HIS   0.006   0.003   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.01151 ( 1317)
  covalent geometry    : angle       1.20579 ( 1761)
  hydrogen bonds       : bond        0.10612 (   16)
  hydrogen bonds       : angle       7.76555 (   48)

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

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

  342 Ramachandran restraints generated.
    171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  342 Ramachandran restraints generated.
    171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.028 
Fit side-chains
REVERT: A  295 ASP cc_start: 0.9033 (p0) cc_final: 0.8773 (p0)
REVERT: C  290 LYS cc_start: 0.8542 (mttt) cc_final: 0.8281 (mmtp)
REVERT: C  315 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8371 (tt)
REVERT: B  294 LYS cc_start: 0.8118 (mttt) cc_final: 0.7503 (mptt)
REVERT: B  295 ASP cc_start: 0.8598 (p0) cc_final: 0.7597 (m-30)
  outliers start: 3
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0415
  time to fit residues: 1.8758
Evaluate side-chains
  21 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  315 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0370
   chunk 7 optimal weight:    6.9990
   chunk 5 optimal weight:    0.0570
   chunk 9 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
A 299 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.146835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.106539 restraints weight = 1600.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3967 rms_B_bonded: 3.39
r_work: 0.3862 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.3756 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   1317  Z= 0.110
  Angle     :  0.584   6.076   1761  Z= 0.298
  Chirality :  0.053   0.127    204
  Planarity :  0.004   0.031    222
  Dihedral  :  6.714  39.076    179
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 1.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 16.34 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.85 (0.47), residues: 171
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.16 (0.36), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR C 310 
 HIS   0.005   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 1317)
  covalent geometry    : angle       0.58448 ( 1761)
  hydrogen bonds       : bond        0.02371 (   16)
  hydrogen bonds       : angle       5.50551 (   48)

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

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

  342 Ramachandran restraints generated.
    171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  342 Ramachandran restraints generated.
    171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.029 
Fit side-chains
REVERT: A  295 ASP cc_start: 0.8893 (p0) cc_final: 0.8618 (p0)
REVERT: A  327 ASN cc_start: 0.7648 (m-40) cc_final: 0.7390 (m-40)
REVERT: C  295 ASP cc_start: 0.8607 (p0) cc_final: 0.8312 (p0)
REVERT: C  315 LEU cc_start: 0.8167 (mt) cc_final: 0.7857 (mt)
REVERT: B  286 ASN cc_start: 0.8845 (t0) cc_final: 0.8458 (t0)
REVERT: B  295 ASP cc_start: 0.8614 (p0) cc_final: 0.7476 (m-30)
  outliers start: 7
  outliers final: 6
  residues processed: 33
  average time/residue: 0.0476
  time to fit residues: 1.7292
Evaluate side-chains
  28 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain B residue  305 SER
Chi-restraints excluded: chain B residue  315 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 3 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 2 optimal weight:   20.0000
   chunk 0 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 299 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.147568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.105931 restraints weight = 1654.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3960 rms_B_bonded: 3.54
r_work: 0.3831 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.2719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   1317  Z= 0.128
  Angle     :  0.557   5.690   1761  Z= 0.283
  Chirality :  0.053   0.128    204
  Planarity :  0.004   0.032    222
  Dihedral  :  5.416  14.777    177
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 1.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 17.65 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.74 (0.49), residues: 171
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.08 (0.37), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR C 310 
 HIS   0.003   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 1317)
  covalent geometry    : angle       0.55674 ( 1761)
  hydrogen bonds       : bond        0.01983 (   16)
  hydrogen bonds       : angle       4.74292 (   48)

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

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

  342 Ramachandran restraints generated.
    171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  342 Ramachandran restraints generated.
    171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 25
  time to evaluate  : 0.031 
Fit side-chains
REVERT: A  295 ASP cc_start: 0.8852 (p0) cc_final: 0.8560 (p0)
REVERT: A  315 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7789 (tt)
REVERT: A  327 ASN cc_start: 0.7828 (m-40) cc_final: 0.7510 (m-40)
REVERT: C  295 ASP cc_start: 0.8738 (p0) cc_final: 0.8341 (p0)
REVERT: C  315 LEU cc_start: 0.8198 (mt) cc_final: 0.7977 (mt)
REVERT: B  286 ASN cc_start: 0.8821 (t0) cc_final: 0.8476 (t0)
REVERT: B  295 ASP cc_start: 0.8757 (p0) cc_final: 0.7589 (m-30)
  outliers start: 7
  outliers final: 5
  residues processed: 30
  average time/residue: 0.0383
  time to fit residues: 1.2959
Evaluate side-chains
  29 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain B residue  305 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 1 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 7 optimal weight:    9.9990
   chunk 0 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 299 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.145076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.102892 restraints weight = 1731.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3922 rms_B_bonded: 3.64
r_work: 0.3796 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.2880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   1317  Z= 0.201
  Angle     :  0.580   5.078   1761  Z= 0.298
  Chirality :  0.053   0.123    204
  Planarity :  0.004   0.033    222
  Dihedral  :  5.427  14.704    177
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 0.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 17.65 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.72 (0.51), residues: 171
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.39), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.011   0.002   TYR C 310 
 HIS   0.003   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 1317)
  covalent geometry    : angle       0.58004 ( 1761)
  hydrogen bonds       : bond        0.02071 (   16)
  hydrogen bonds       : angle       4.38758 (   48)

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

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

  342 Ramachandran restraints generated.
    171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  342 Ramachandran restraints generated.
    171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 25
  time to evaluate  : 0.030 
Fit side-chains
REVERT: A  295 ASP cc_start: 0.8788 (p0) cc_final: 0.8510 (p0)
REVERT: A  327 ASN cc_start: 0.7826 (m-40) cc_final: 0.7442 (m-40)
REVERT: C  295 ASP cc_start: 0.8681 (p0) cc_final: 0.8283 (p0)
REVERT: B  274 LYS cc_start: 0.8487 (mtpt) cc_final: 0.8112 (ttmt)
REVERT: B  286 ASN cc_start: 0.8855 (t0) cc_final: 0.8334 (t0)
REVERT: B  295 ASP cc_start: 0.8720 (p0) cc_final: 0.7497 (m-30)
REVERT: B  315 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8051 (mt)
  outliers start: 7
  outliers final: 3
  residues processed: 30
  average time/residue: 0.0399
  time to fit residues: 1.3434
Evaluate side-chains
  28 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain B residue  305 SER
Chi-restraints excluded: chain B residue  315 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 12 optimal weight:   20.0000
   chunk 3 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 299 HIS
B 288 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.144690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.102835 restraints weight = 1691.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3934 rms_B_bonded: 3.64
r_work: 0.3807 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.3087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   1317  Z= 0.215
  Angle     :  0.625   7.644   1761  Z= 0.311
  Chirality :  0.053   0.122    204
  Planarity :  0.004   0.033    222
  Dihedral  :  5.352  13.974    177
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 0.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 16.99 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.79 (0.52), residues: 171
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.40), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.002   TYR C 310 
 HIS   0.003   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 ( 1317)
  covalent geometry    : angle       0.62513 ( 1761)
  hydrogen bonds       : bond        0.02096 (   16)
  hydrogen bonds       : angle       4.33789 (   48)

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

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

  342 Ramachandran restraints generated.
    171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  342 Ramachandran restraints generated.
    171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 18
  time to evaluate  : 0.030 
Fit side-chains
REVERT: A  295 ASP cc_start: 0.8780 (p0) cc_final: 0.8503 (p0)
REVERT: A  327 ASN cc_start: 0.7841 (m-40) cc_final: 0.7495 (m-40)
REVERT: C  295 ASP cc_start: 0.8662 (p0) cc_final: 0.8262 (p0)
REVERT: C  314 ASP cc_start: 0.7362 (m-30) cc_final: 0.6528 (t0)
REVERT: B  295 ASP cc_start: 0.8642 (p0) cc_final: 0.7221 (m-30)
  outliers start: 5
  outliers final: 5
  residues processed: 22
  average time/residue: 0.0438
  time to fit residues: 1.0856
Evaluate side-chains
  23 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 18
  time to evaluate  : 0.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain B residue  288 GLN
Chi-restraints excluded: chain B residue  305 SER
Chi-restraints excluded: chain B residue  315 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 7 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0870
   chunk 4 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.9560

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

Flipped N/Q/H residues before XYZ refinement:
B 288 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.148301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.106583 restraints weight = 1596.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3975 rms_B_bonded: 3.52
r_work: 0.3852 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   1317  Z= 0.118
  Angle     :  0.549   5.525   1761  Z= 0.275
  Chirality :  0.053   0.126    204
  Planarity :  0.004   0.032    222
  Dihedral  :  5.128  14.232    177
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 1.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 16.99 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.72 (0.52), residues: 171
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.06 (0.40), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR C 310 
 HIS   0.003   0.000   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 1317)
  covalent geometry    : angle       0.54857 ( 1761)
  hydrogen bonds       : bond        0.01646 (   16)
  hydrogen bonds       : angle       4.30561 (   48)

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

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

  342 Ramachandran restraints generated.
    171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  342 Ramachandran restraints generated.
    171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.060 
Fit side-chains
REVERT: A  295 ASP cc_start: 0.8885 (p0) cc_final: 0.8631 (p0)
REVERT: A  327 ASN cc_start: 0.7897 (m-40) cc_final: 0.7547 (m-40)
REVERT: C  314 ASP cc_start: 0.7272 (m-30) cc_final: 0.6549 (t0)
REVERT: B  274 LYS cc_start: 0.8370 (mtpt) cc_final: 0.8029 (ttmt)
REVERT: B  295 ASP cc_start: 0.8637 (p0) cc_final: 0.7166 (m-30)
  outliers start: 5
  outliers final: 4
  residues processed: 25
  average time/residue: 0.0837
  time to fit residues: 2.3187
Evaluate side-chains
  24 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 20
  time to evaluate  : 0.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain B residue  288 GLN
Chi-restraints excluded: chain B residue  305 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9980
   chunk 12 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    1.0784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.147639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.105966 restraints weight = 1608.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3976 rms_B_bonded: 3.50
r_work: 0.3853 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.3294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   1317  Z= 0.125
  Angle     :  0.545   6.330   1761  Z= 0.271
  Chirality :  0.053   0.124    204
  Planarity :  0.004   0.031    222
  Dihedral  :  5.008  13.850    177
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 0.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 18.30 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.59 (0.53), residues: 171
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.41), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR C 310 
 HIS   0.003   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 1317)
  covalent geometry    : angle       0.54536 ( 1761)
  hydrogen bonds       : bond        0.01609 (   16)
  hydrogen bonds       : angle       4.17956 (   48)

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

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

  342 Ramachandran restraints generated.
    171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  342 Ramachandran restraints generated.
    171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.061 
Fit side-chains
REVERT: A  295 ASP cc_start: 0.8916 (p0) cc_final: 0.8583 (p0)
REVERT: A  327 ASN cc_start: 0.7977 (m-40) cc_final: 0.7600 (m-40)
REVERT: C  295 ASP cc_start: 0.8419 (p0) cc_final: 0.8116 (p0)
REVERT: C  314 ASP cc_start: 0.7226 (m-30) cc_final: 0.6590 (t0)
REVERT: B  274 LYS cc_start: 0.8314 (mtpt) cc_final: 0.8020 (ttmt)
REVERT: B  293 SER cc_start: 0.7604 (p) cc_final: 0.7348 (p)
REVERT: B  295 ASP cc_start: 0.8654 (p0) cc_final: 0.7244 (m-30)
  outliers start: 4
  outliers final: 3
  residues processed: 27
  average time/residue: 0.0804
  time to fit residues: 2.4219
Evaluate side-chains
  25 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain B residue  305 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 8 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 5 optimal weight:    0.1980
   chunk 9 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 0 optimal weight:    0.6980
   chunk 12 optimal weight:    0.2980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B 288 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.152710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.110514 restraints weight = 1564.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.4051 rms_B_bonded: 3.54
r_work: 0.3933 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.3539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   1317  Z= 0.087
  Angle     :  0.534   8.069   1761  Z= 0.256
  Chirality :  0.053   0.127    204
  Planarity :  0.003   0.030    222
  Dihedral  :  4.685  13.855    177
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 0.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 20.92 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.51 (0.55), residues: 171
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.91 (0.42), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR C 310 
 HIS   0.003   0.000   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00188 ( 1317)
  covalent geometry    : angle       0.53438 ( 1761)
  hydrogen bonds       : bond        0.01331 (   16)
  hydrogen bonds       : angle       4.09733 (   48)

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

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

  342 Ramachandran restraints generated.
    171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  342 Ramachandran restraints generated.
    171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.061 
Fit side-chains
REVERT: A  295 ASP cc_start: 0.8734 (p0) cc_final: 0.8462 (p0)
REVERT: A  327 ASN cc_start: 0.7974 (m-40) cc_final: 0.7574 (m-40)
REVERT: C  294 LYS cc_start: 0.8224 (mttt) cc_final: 0.6722 (mmtt)
REVERT: C  299 HIS cc_start: 0.8052 (m90) cc_final: 0.7779 (m90)
REVERT: C  314 ASP cc_start: 0.7209 (m-30) cc_final: 0.6792 (t0)
REVERT: B  274 LYS cc_start: 0.8229 (mtpt) cc_final: 0.7996 (ttmt)
REVERT: B  293 SER cc_start: 0.7558 (p) cc_final: 0.7254 (p)
REVERT: B  295 ASP cc_start: 0.8698 (p0) cc_final: 0.7165 (m-30)
REVERT: B  314 ASP cc_start: 0.6778 (m-30) cc_final: 0.6047 (t0)
REVERT: B  317 LYS cc_start: 0.8287 (mttt) cc_final: 0.7936 (ttmt)
  outliers start: 2
  outliers final: 1
  residues processed: 27
  average time/residue: 0.0930
  time to fit residues: 2.7538
Evaluate side-chains
  26 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  305 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 2 optimal weight:   30.0000
   chunk 6 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 11 optimal weight:    0.4980
   overall best weight:    1.2584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.153165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.110801 restraints weight = 1650.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.4018 rms_B_bonded: 3.58
r_work: 0.3885 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.3643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   1317  Z= 0.140
  Angle     :  0.546   8.136   1761  Z= 0.265
  Chirality :  0.052   0.123    204
  Planarity :  0.003   0.028    222
  Dihedral  :  4.772  13.518    177
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 1.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 18.30 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.46 (0.56), residues: 171
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.87 (0.42), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.002   TYR C 310 
 HIS   0.002   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 1317)
  covalent geometry    : angle       0.54621 ( 1761)
  hydrogen bonds       : bond        0.01547 (   16)
  hydrogen bonds       : angle       3.94169 (   48)

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

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

  342 Ramachandran restraints generated.
    171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  342 Ramachandran restraints generated.
    171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.053 
Fit side-chains
REVERT: A  327 ASN cc_start: 0.7950 (m-40) cc_final: 0.7542 (m-40)
REVERT: C  276 GLN cc_start: 0.8114 (mt0) cc_final: 0.7381 (tt0)
REVERT: C  299 HIS cc_start: 0.8091 (m90) cc_final: 0.7819 (m90)
REVERT: C  314 ASP cc_start: 0.7073 (m-30) cc_final: 0.6642 (t0)
REVERT: B  274 LYS cc_start: 0.8235 (mtpt) cc_final: 0.7992 (ttmt)
REVERT: B  293 SER cc_start: 0.7542 (p) cc_final: 0.7241 (p)
REVERT: B  295 ASP cc_start: 0.8703 (p0) cc_final: 0.7179 (m-30)
REVERT: B  314 ASP cc_start: 0.6796 (m-30) cc_final: 0.6042 (t0)
REVERT: B  317 LYS cc_start: 0.8310 (mttt) cc_final: 0.7962 (ttmt)
  outliers start: 3
  outliers final: 3
  residues processed: 27
  average time/residue: 0.0800
  time to fit residues: 2.3920
Evaluate side-chains
  27 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain B residue  305 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 7 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 12 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.9588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.149221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.106805 restraints weight = 1681.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3946 rms_B_bonded: 3.61
r_work: 0.3821 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.3665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   1317  Z= 0.192
  Angle     :  0.600   9.310   1761  Z= 0.293
  Chirality :  0.053   0.120    204
  Planarity :  0.004   0.029    222
  Dihedral  :  4.941  13.315    177
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 1.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 19.61 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.50 (0.55), residues: 171
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.90 (0.42), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.011   0.002   TYR C 310 
 HIS   0.002   0.001   HIS A 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 1317)
  covalent geometry    : angle       0.60019 ( 1761)
  hydrogen bonds       : bond        0.01755 (   16)
  hydrogen bonds       : angle       3.98174 (   48)

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

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

  342 Ramachandran restraints generated.
    171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  342 Ramachandran restraints generated.
    171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.057 
Fit side-chains
REVERT: A  327 ASN cc_start: 0.7993 (m-40) cc_final: 0.7613 (m-40)
REVERT: C  276 GLN cc_start: 0.8146 (mt0) cc_final: 0.7432 (tt0)
REVERT: C  299 HIS cc_start: 0.8133 (m90) cc_final: 0.7868 (m90)
REVERT: C  314 ASP cc_start: 0.7027 (m-30) cc_final: 0.6599 (t0)
REVERT: B  274 LYS cc_start: 0.8308 (mtpt) cc_final: 0.8052 (ttmt)
REVERT: B  295 ASP cc_start: 0.8721 (p0) cc_final: 0.7343 (m-30)
REVERT: B  314 ASP cc_start: 0.6818 (m-30) cc_final: 0.6033 (t0)
REVERT: B  317 LYS cc_start: 0.8350 (mttt) cc_final: 0.7981 (ttmt)
  outliers start: 3
  outliers final: 3
  residues processed: 28
  average time/residue: 0.0898
  time to fit residues: 2.7564
Evaluate side-chains
  28 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain B residue  305 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 12 optimal weight:   20.0000
   chunk 2 optimal weight:   20.0000
   chunk 14 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 3 optimal weight:    0.2980
   chunk 8 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.7782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.149284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.107128 restraints weight = 1583.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.4002 rms_B_bonded: 3.53
r_work: 0.3878 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.3815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   1317  Z= 0.108
  Angle     :  0.541   7.688   1761  Z= 0.263
  Chirality :  0.053   0.126    204
  Planarity :  0.004   0.030    222
  Dihedral  :  4.687  13.525    177
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 1.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 20.92 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.44 (0.56), residues: 171
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.43), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR C 310 
 HIS   0.002   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 1317)
  covalent geometry    : angle       0.54070 ( 1761)
  hydrogen bonds       : bond        0.01392 (   16)
  hydrogen bonds       : angle       3.94811 (   48)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 561.96 seconds
wall clock time: 10 minutes 32.51 seconds (632.51 seconds total)