Starting phenix.real_space_refine
on Wed Mar  5 14:17:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qjh_4563/03_2025/6qjh_4563.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qjh_4563/03_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_4563/03_2025/6qjh_4563.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qjh_4563/03_2025/6qjh_4563.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qjh_4563/03_2025/6qjh_4563.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qjh_4563/03_2025/6qjh_4563.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 0.98, per 1000 atoms: 0.75
  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: 0.68
  Conformation dependent library (CDL) restraints added in 144.1 milliseconds
  

  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: 0.20
  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: 0.36

  Time building geometry restraints manager: 0.74 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: 0.01
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:             0.740
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.390
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.170
-------------------------------------------------------------------------------
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= 0.810
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 HIS   0.006   0.003   HIS A 299 
 TYR   0.011   0.004   TYR A 310 

*********************** 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  : 0.161 
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: 0.1759
  time to fit residues: 7.9791
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  : 0.170 
-------------------------------------------------------------------------------
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 12 optimal weight:    7.9990
   chunk 11 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.4352 r_free = 0.4352 target = 0.145015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.104798 restraints weight = 1626.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3923 rms_B_bonded: 3.37
r_work: 0.3800 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3680 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.2205

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= 0.215
  Angle     :  0.603   6.088   1761  Z= 0.309
  Chirality :  0.053   0.125    204
  Planarity :  0.004   0.032    222
  Dihedral  :  6.978  41.270    179
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 1.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 15.69 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.90 (0.47), residues: 171
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.20 (0.36), residues: 171

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

*********************** 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
  34 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 27
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A  295 ASP cc_start: 0.8837 (p0) cc_final: 0.8573 (p0)
REVERT: A  327 ASN cc_start: 0.7762 (m-40) cc_final: 0.7434 (m-40)
REVERT: C  290 LYS cc_start: 0.8561 (mttt) cc_final: 0.8114 (mmtp)
REVERT: C  295 ASP cc_start: 0.8520 (p0) cc_final: 0.8264 (p0)
REVERT: C  315 LEU cc_start: 0.8239 (mt) cc_final: 0.7911 (mt)
REVERT: B  286 ASN cc_start: 0.8876 (t0) cc_final: 0.8504 (t0)
REVERT: B  295 ASP cc_start: 0.8527 (p0) cc_final: 0.7471 (m-30)
  outliers start: 7
  outliers final: 6
  residues processed: 32
  average time/residue: 0.1387
  time to fit residues: 5.0272
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  : 0.148 
-------------------------------------------------------------------------------
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 8 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 2 optimal weight:   20.0000
   chunk 11 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 299 HIS
B 286 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.150007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.108312 restraints weight = 1601.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3999 rms_B_bonded: 3.53
r_work: 0.3873 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.2848

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= 0.175
  Angle     :  0.538   5.667   1761  Z= 0.273
  Chirality :  0.053   0.129    204
  Planarity :  0.004   0.033    222
  Dihedral  :  5.247  14.691    177
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 1.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.76 (0.49), residues: 171
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (0.38), residues: 171

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

*********************** 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
  34 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 27
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A  295 ASP cc_start: 0.8916 (p0) cc_final: 0.8644 (p0)
REVERT: A  315 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7813 (tt)
REVERT: A  327 ASN cc_start: 0.7850 (m-40) cc_final: 0.7460 (m-40)
REVERT: C  295 ASP cc_start: 0.8757 (p0) cc_final: 0.8351 (p0)
REVERT: C  314 ASP cc_start: 0.7088 (m-30) cc_final: 0.6415 (t0)
REVERT: C  315 LEU cc_start: 0.8143 (mt) cc_final: 0.7887 (mt)
REVERT: B  286 ASN cc_start: 0.8768 (t0) cc_final: 0.8081 (t0)
REVERT: B  295 ASP cc_start: 0.8729 (p0) cc_final: 0.7491 (m-30)
  outliers start: 7
  outliers final: 3
  residues processed: 32
  average time/residue: 0.1420
  time to fit residues: 5.1107
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  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  324 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 5 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 7 optimal weight:    9.9990
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0870
   overall best weight:    0.9964

-------------------------------------------------------------------------------
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 = 0.4428 r_free = 0.4428 target = 0.149462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.107580 restraints weight = 1602.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3987 rms_B_bonded: 3.54
r_work: 0.3858 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.3050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015   1317  Z= 0.186
  Angle     :  0.518   4.798   1761  Z= 0.264
  Chirality :  0.052   0.123    204
  Planarity :  0.004   0.032    222
  Dihedral  :  5.062  14.540    177
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 0.75
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.66 (0.51), residues: 171
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.02 (0.39), residues: 171

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

*********************** 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
  29 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 24
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A  295 ASP cc_start: 0.8933 (p0) cc_final: 0.8661 (p0)
REVERT: A  327 ASN cc_start: 0.7930 (m-40) cc_final: 0.7501 (m-40)
REVERT: C  276 GLN cc_start: 0.8109 (mt0) cc_final: 0.7407 (tt0)
REVERT: C  295 ASP cc_start: 0.8829 (p0) cc_final: 0.8422 (p0)
REVERT: C  314 ASP cc_start: 0.7097 (m-30) cc_final: 0.6406 (t0)
REVERT: B  286 ASN cc_start: 0.8814 (t0) cc_final: 0.8332 (t0)
REVERT: B  295 ASP cc_start: 0.8780 (p0) cc_final: 0.7459 (m-30)
  outliers start: 5
  outliers final: 3
  residues processed: 28
  average time/residue: 0.1409
  time to fit residues: 4.5425
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  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain B residue  305 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 3 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 2 optimal weight:   20.0000
   chunk 6 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 299 HIS
B 286 ASN
B 288 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.151286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.109412 restraints weight = 1552.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.4029 rms_B_bonded: 3.54
r_work: 0.3899 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.3275

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= 0.173
  Angle     :  0.510   4.381   1761  Z= 0.256
  Chirality :  0.052   0.124    204
  Planarity :  0.004   0.032    222
  Dihedral  :  4.826  14.263    177
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 0.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 15.69 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.62 (0.52), residues: 171
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.99 (0.40), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 299 
 TYR   0.004   0.001   TYR C 310 

*********************** 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
  29 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A  295 ASP cc_start: 0.8855 (p0) cc_final: 0.8570 (p0)
REVERT: A  327 ASN cc_start: 0.7927 (m-40) cc_final: 0.7500 (m-40)
REVERT: C  276 GLN cc_start: 0.8150 (mt0) cc_final: 0.7416 (tt0)
REVERT: C  295 ASP cc_start: 0.8805 (p0) cc_final: 0.8392 (p0)
REVERT: C  314 ASP cc_start: 0.7190 (m-30) cc_final: 0.6492 (t0)
REVERT: B  295 ASP cc_start: 0.8746 (p0) cc_final: 0.7604 (m-30)
REVERT: B  314 ASP cc_start: 0.6679 (m-30) cc_final: 0.5844 (t0)
  outliers start: 6
  outliers final: 5
  residues processed: 28
  average time/residue: 0.1476
  time to fit residues: 4.7313
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  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  288 GLN
Chi-restraints excluded: chain B residue  305 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 12 optimal weight:   20.0000
   chunk 4 optimal weight:    0.9990
   chunk 2 optimal weight:    8.9990
   overall best weight:    1.5786

-------------------------------------------------------------------------------
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 = 0.4451 r_free = 0.4451 target = 0.152089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.109784 restraints weight = 1622.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.4009 rms_B_bonded: 3.58
r_work: 0.3879 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.3330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   1317  Z= 0.248
  Angle     :  0.562   7.731   1761  Z= 0.278
  Chirality :  0.053   0.123    204
  Planarity :  0.004   0.030    222
  Dihedral  :  4.837  13.930    177
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 0.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 18.95 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.57 (0.53), residues: 171
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.95 (0.41), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 299 
 TYR   0.008   0.002   TYR C 310 

*********************** 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
  25 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A  295 ASP cc_start: 0.8812 (p0) cc_final: 0.8464 (p0)
REVERT: A  327 ASN cc_start: 0.7899 (m-40) cc_final: 0.7496 (m-40)
REVERT: C  276 GLN cc_start: 0.8163 (mt0) cc_final: 0.7390 (tt0)
REVERT: C  295 ASP cc_start: 0.8774 (p0) cc_final: 0.8382 (p0)
REVERT: C  314 ASP cc_start: 0.7104 (m-30) cc_final: 0.6499 (t0)
REVERT: B  274 LYS cc_start: 0.8345 (mtpt) cc_final: 0.8080 (ttmt)
REVERT: B  295 ASP cc_start: 0.8556 (p0) cc_final: 0.7082 (m-30)
REVERT: B  297 ILE cc_start: 0.8208 (mt) cc_final: 0.7925 (mp)
  outliers start: 4
  outliers final: 3
  residues processed: 25
  average time/residue: 0.1560
  time to fit residues: 4.4279
Evaluate side-chains
  23 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 20
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 2 optimal weight:   30.0000
   chunk 12 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 7 optimal weight:   30.0000
   overall best weight:    1.5784

-------------------------------------------------------------------------------
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 = 0.4457 r_free = 0.4457 target = 0.151220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.109307 restraints weight = 1692.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3999 rms_B_bonded: 3.60
r_work: 0.3861 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.3414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   1317  Z= 0.246
  Angle     :  0.558   7.431   1761  Z= 0.276
  Chirality :  0.052   0.122    204
  Planarity :  0.004   0.030    222
  Dihedral  :  4.862  13.637    177
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 0.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 18.95 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.45 (0.55), residues: 171
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.86 (0.42), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 299 
 TYR   0.009   0.002   TYR C 310 

*********************** 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
  22 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 19
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A  295 ASP cc_start: 0.8722 (p0) cc_final: 0.8450 (p0)
REVERT: A  327 ASN cc_start: 0.7891 (m-40) cc_final: 0.7461 (m-40)
REVERT: C  295 ASP cc_start: 0.8723 (p0) cc_final: 0.8349 (p0)
REVERT: C  299 HIS cc_start: 0.8093 (m90) cc_final: 0.7829 (m90)
REVERT: C  314 ASP cc_start: 0.7119 (m-30) cc_final: 0.6598 (t0)
REVERT: B  274 LYS cc_start: 0.8326 (mtpt) cc_final: 0.8066 (ttmt)
REVERT: B  295 ASP cc_start: 0.8413 (p0) cc_final: 0.6723 (m-30)
  outliers start: 3
  outliers final: 3
  residues processed: 22
  average time/residue: 0.1771
  time to fit residues: 4.3868
Evaluate side-chains
  22 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 19
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
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 6 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 2 optimal weight:   30.0000
   overall best weight:    1.3788

-------------------------------------------------------------------------------
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 = 0.4450 r_free = 0.4450 target = 0.151158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.108932 restraints weight = 1631.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3997 rms_B_bonded: 3.57
r_work: 0.3868 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.3563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   1317  Z= 0.219
  Angle     :  0.536   6.867   1761  Z= 0.265
  Chirality :  0.052   0.122    204
  Planarity :  0.004   0.031    222
  Dihedral  :  4.774  13.609    177
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 0.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 18.95 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.37 (0.56), residues: 171
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.43), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 299 
 TYR   0.008   0.002   TYR C 310 

*********************** 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
  24 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A  295 ASP cc_start: 0.8721 (p0) cc_final: 0.8510 (p0)
REVERT: A  327 ASN cc_start: 0.7941 (m-40) cc_final: 0.7516 (m-40)
REVERT: C  295 ASP cc_start: 0.8714 (p0) cc_final: 0.8447 (p0)
REVERT: C  299 HIS cc_start: 0.8076 (m90) cc_final: 0.7801 (m90)
REVERT: C  314 ASP cc_start: 0.6970 (m-30) cc_final: 0.6596 (t0)
REVERT: B  274 LYS cc_start: 0.8277 (mtpt) cc_final: 0.8033 (ttmt)
REVERT: B  295 ASP cc_start: 0.8391 (p0) cc_final: 0.6793 (m-30)
REVERT: B  314 ASP cc_start: 0.6772 (m-30) cc_final: 0.6048 (t0)
  outliers start: 3
  outliers final: 3
  residues processed: 24
  average time/residue: 0.1646
  time to fit residues: 4.4530
Evaluate side-chains
  24 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    9.9990
   chunk 1 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   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 = 0.4455 r_free = 0.4455 target = 0.151175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.108563 restraints weight = 1620.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3998 rms_B_bonded: 3.59
r_work: 0.3867 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.3706

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= 0.186
  Angle     :  0.514   6.390   1761  Z= 0.254
  Chirality :  0.052   0.123    204
  Planarity :  0.004   0.031    222
  Dihedral  :  4.684  13.579    177
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 1.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.37 (0.57), residues: 171
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.43), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 299 
 TYR   0.007   0.001   TYR C 310 

*********************** 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
  24 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A  295 ASP cc_start: 0.8693 (p0) cc_final: 0.8476 (p0)
REVERT: A  327 ASN cc_start: 0.7940 (m-40) cc_final: 0.7542 (m-40)
REVERT: C  295 ASP cc_start: 0.8681 (p0) cc_final: 0.8409 (p0)
REVERT: C  299 HIS cc_start: 0.8121 (m90) cc_final: 0.7845 (m90)
REVERT: C  314 ASP cc_start: 0.6862 (m-30) cc_final: 0.6539 (t0)
REVERT: B  274 LYS cc_start: 0.8230 (mtpt) cc_final: 0.8021 (ttmt)
REVERT: B  295 ASP cc_start: 0.8463 (p0) cc_final: 0.6923 (m-30)
REVERT: B  314 ASP cc_start: 0.6797 (m-30) cc_final: 0.5902 (t0)
  outliers start: 3
  outliers final: 3
  residues processed: 24
  average time/residue: 0.1584
  time to fit residues: 4.3175
Evaluate side-chains
  24 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
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 10 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 3 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 12 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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 = 0.4460 r_free = 0.4460 target = 0.151139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.108498 restraints weight = 1652.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3997 rms_B_bonded: 3.60
r_work: 0.3863 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.3752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   1317  Z= 0.214
  Angle     :  0.521   6.537   1761  Z= 0.258
  Chirality :  0.052   0.122    204
  Planarity :  0.004   0.031    222
  Dihedral  :  4.687  13.439    177
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 1.12
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.35 (0.57), residues: 171
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.43), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 299 
 TYR   0.008   0.002   TYR C 310 

********************** 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
  25 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A  295 ASP cc_start: 0.8672 (p0) cc_final: 0.8461 (p0)
REVERT: A  327 ASN cc_start: 0.7959 (m-40) cc_final: 0.7548 (m-40)
REVERT: C  295 ASP cc_start: 0.8643 (p0) cc_final: 0.8372 (p0)
REVERT: C  299 HIS cc_start: 0.8132 (m90) cc_final: 0.7880 (m90)
REVERT: C  314 ASP cc_start: 0.6916 (m-30) cc_final: 0.6590 (t0)
REVERT: B  274 LYS cc_start: 0.8250 (mtpt) cc_final: 0.8040 (ttmt)
REVERT: B  295 ASP cc_start: 0.8480 (p0) cc_final: 0.6952 (m-30)
REVERT: B  314 ASP cc_start: 0.6796 (m-30) cc_final: 0.5913 (t0)
  outliers start: 3
  outliers final: 3
  residues processed: 25
  average time/residue: 0.1803
  time to fit residues: 5.0962
Evaluate side-chains
  24 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
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 2 optimal weight:   30.0000
   chunk 9 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 7 optimal weight:    7.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    2.3786

-------------------------------------------------------------------------------
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 = 0.4425 r_free = 0.4425 target = 0.145086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.102884 restraints weight = 1659.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3939 rms_B_bonded: 3.55
r_work: 0.3814 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.3749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   1317  Z= 0.341
  Angle     :  0.586   6.967   1761  Z= 0.295
  Chirality :  0.053   0.129    204
  Planarity :  0.004   0.031    222
  Dihedral  :  4.947  13.295    177
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 0.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 18.95 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.40 (0.56), residues: 171
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.82 (0.43), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 329 
 TYR   0.013   0.003   TYR C 310 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1188.08 seconds
wall clock time: 21 minutes 6.20 seconds (1266.20 seconds total)