Starting phenix.real_space_refine
on Sun Apr 27 05:36:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8orf_17122/04_2025/8orf_17122.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8orf_17122/04_2025/8orf_17122.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8orf_17122/04_2025/8orf_17122.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8orf_17122/04_2025/8orf_17122.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8orf_17122/04_2025/8orf_17122.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8orf_17122/04_2025/8orf_17122.cif"
  }
  resolution = 2.5
  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=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    1413      2.51       5
     N     420      2.21       5
     O     432      1.98       5
     H    2382      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 4653
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1551
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 1551
          Classifications: {'peptide': 101}
          Link IDs: {'PTRANS': 4, 'TRANS': 96}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 2.57, per 1000 atoms: 0.55
  Number of scatterers: 4653
  At special positions: 0
  Unit cell: (83.93, 92.65, 35.97, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       6     16.00
     O     432      8.00
     N     420      7.00
     C    1413      6.00
     H    2382      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Conformation dependent library (CDL) restraints added in 297.8 milliseconds
  

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  528

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 45.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 278 through 283
      removed outlier: 6.421A  pdb=" N   ILE B 278 " --> pdb=" O   ASN C 279 " (cutoff:3.500A)
      removed outlier: 8.121A  pdb=" N   LYS C 281 " --> pdb=" O   ILE B 278 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   LYS B 280 " --> pdb=" O   LYS C 281 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   ASP C 283 " --> pdb=" O   LYS B 280 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   LEU B 282 " --> pdb=" O   ASP C 283 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 286 through 289
    Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 299
      removed outlier: 6.432A  pdb=" N   ILE B 297 " --> pdb=" O   LYS C 298 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 310
      removed outlier: 6.822A  pdb=" N   GLY B 304 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   GLY B 303 " --> pdb=" O   GLY C 304 " (cutoff:3.500A)
      removed outlier: 8.419A  pdb=" N   VAL C 306 " --> pdb=" O   GLY B 303 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   SER B 305 " --> pdb=" O   VAL C 306 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   ILE C 308 " --> pdb=" O   SER B 305 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   GLN B 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 7.706A  pdb=" N   TYR C 310 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   VAL B 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 318
      removed outlier: 6.397A  pdb=" N   VAL B 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
      removed outlier: 7.783A  pdb=" N   SER C 316 " --> pdb=" O   VAL B 313 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   LEU B 315 " --> pdb=" O   SER C 316 " (cutoff:3.500A)
      removed outlier: 7.810A  pdb=" N   VAL C 318 " --> pdb=" O   LEU B 315 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   LYS B 317 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 321 through 322
      removed outlier: 6.733A  pdb=" N   LYS B 321 " --> pdb=" O   CYS C 322 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 327 through 330
      removed outlier: 6.456A  pdb=" N   ASN B 327 " --> pdb=" O   ILE C 328 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   HIS C 330 " --> pdb=" O   ASN B 327 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   HIS B 329 " --> pdb=" O   HIS C 330 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 336 through 341
      removed outlier: 6.360A  pdb=" N   VAL B 337 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 7.818A  pdb=" N   LYS A 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   VAL B 339 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 344 through 346
      removed outlier: 6.539A  pdb=" N   ASP B 345 " --> pdb=" O   PHE C 346 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 350 through 354
      removed outlier: 6.272A  pdb=" N   VAL B 350 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 8.002A  pdb=" N   LYS A 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   SER B 352 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 360 through 361
      removed outlier: 6.632A  pdb=" N   ILE B 360 " --> pdb=" O   THR A 361 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 369 through 376
      removed outlier: 6.908A  pdb=" N   LYS B 370 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   LYS A 375 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   LEU B 376 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   ILE C 371 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   GLU B 372 " --> pdb=" O   ILE C 371 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   THR C 373 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   HIS B 374 " --> pdb=" O   THR C 373 " (cutoff:3.500A)

    48 hydrogen bonds defined for protein.
    144 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: 1.46

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 2376
        1.03 -     1.22: 6
        1.22 -     1.41: 867
        1.41 -     1.61: 1428
        1.61 -     1.80: 6
  Bond restraints: 4683
  Sorted by residual:
  bond pdb=" CG  LYS B 311 "
       pdb=" HG3 LYS B 311 "
    ideal  model  delta    sigma   weight residual
    0.970  0.938  0.032 2.00e-02 2.50e+03 2.62e+00
  bond pdb=" CG  LYS C 311 "
       pdb=" HG3 LYS C 311 "
    ideal  model  delta    sigma   weight residual
    0.970  0.938  0.032 2.00e-02 2.50e+03 2.62e+00
  bond pdb=" CG  LYS A 311 "
       pdb=" HG3 LYS A 311 "
    ideal  model  delta    sigma   weight residual
    0.970  0.938  0.032 2.00e-02 2.50e+03 2.60e+00
  bond pdb=" CE  LYS A 311 "
       pdb=" NZ  LYS A 311 "
    ideal  model  delta    sigma   weight residual
    1.489  1.441  0.048 3.00e-02 1.11e+03 2.58e+00
  bond pdb=" CE  LYS C 311 "
       pdb=" NZ  LYS C 311 "
    ideal  model  delta    sigma   weight residual
    1.489  1.441  0.048 3.00e-02 1.11e+03 2.54e+00
  ... (remaining 4678 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 7441
        1.60 -     3.20: 937
        3.20 -     4.80: 151
        4.80 -     6.40: 18
        6.40 -     8.01: 12
  Bond angle restraints: 8559
  Sorted by residual:
  angle pdb=" CA  LYS B 281 "
        pdb=" CB  LYS B 281 "
        pdb=" CG  LYS B 281 "
      ideal   model   delta    sigma   weight residual
     114.10  120.85   -6.75 2.00e+00 2.50e-01 1.14e+01
  angle pdb=" CA  LYS C 281 "
        pdb=" CB  LYS C 281 "
        pdb=" CG  LYS C 281 "
      ideal   model   delta    sigma   weight residual
     114.10  120.84   -6.74 2.00e+00 2.50e-01 1.14e+01
  angle pdb=" CA  LYS A 281 "
        pdb=" CB  LYS A 281 "
        pdb=" CG  LYS A 281 "
      ideal   model   delta    sigma   weight residual
     114.10  120.77   -6.67 2.00e+00 2.50e-01 1.11e+01
  angle pdb=" CB  LYS B 280 "
        pdb=" CG  LYS B 280 "
        pdb=" CD  LYS B 280 "
      ideal   model   delta    sigma   weight residual
     111.30  118.92   -7.62 2.30e+00 1.89e-01 1.10e+01
  angle pdb=" N   LYS A 281 "
        pdb=" CA  LYS A 281 "
        pdb=" C   LYS A 281 "
      ideal   model   delta    sigma   weight residual
     109.23  114.36   -5.13 1.55e+00 4.16e-01 1.10e+01
  ... (remaining 8554 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.40: 1836
       13.40 -    26.80: 159
       26.80 -    40.20: 45
       40.20 -    53.59: 46
       53.59 -    66.99: 65
  Dihedral angle restraints: 2151
    sinusoidal: 1248
      harmonic: 903
  Sorted by residual:
  dihedral pdb=" CA  SER A 356 "
           pdb=" C   SER A 356 "
           pdb=" N   LEU A 357 "
           pdb=" CA  LEU A 357 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.79   24.21     0      5.00e+00 4.00e-02 2.34e+01
  dihedral pdb=" CA  SER B 356 "
           pdb=" C   SER B 356 "
           pdb=" N   LEU B 357 "
           pdb=" CA  LEU B 357 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.83   24.17     0      5.00e+00 4.00e-02 2.34e+01
  dihedral pdb=" CA  SER C 356 "
           pdb=" C   SER C 356 "
           pdb=" N   LEU C 357 "
           pdb=" CA  LEU C 357 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.86   24.14     0      5.00e+00 4.00e-02 2.33e+01
  ... (remaining 2148 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.049: 178
       0.049 -    0.098: 128
       0.098 -    0.147: 30
       0.147 -    0.195: 11
       0.195 -    0.244: 4
  Chirality restraints: 351
  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    2.27    0.24 2.00e-01 2.50e+01 1.49e+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    2.27    0.24 2.00e-01 2.50e+01 1.43e+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    2.27    0.24 2.00e-01 2.50e+01 1.43e+00
  ... (remaining 348 not shown)

  Planarity restraints: 681
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C 359 "   -0.035 2.00e-02 2.50e+03   5.29e-02 4.20e+01
        pdb=" CG  ASN C 359 "    0.008 2.00e-02 2.50e+03
        pdb=" OD1 ASN C 359 "    0.012 2.00e-02 2.50e+03
        pdb=" ND2 ASN C 359 "    0.092 2.00e-02 2.50e+03
        pdb="HD21 ASN C 359 "    0.006 2.00e-02 2.50e+03
        pdb="HD22 ASN C 359 "   -0.082 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 359 "   -0.035 2.00e-02 2.50e+03   5.26e-02 4.15e+01
        pdb=" CG  ASN B 359 "    0.008 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 359 "    0.011 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 359 "    0.092 2.00e-02 2.50e+03
        pdb="HD21 ASN B 359 "    0.005 2.00e-02 2.50e+03
        pdb="HD22 ASN B 359 "   -0.082 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 359 "   -0.035 2.00e-02 2.50e+03   5.25e-02 4.14e+01
        pdb=" CG  ASN A 359 "    0.008 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 359 "    0.011 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 359 "    0.092 2.00e-02 2.50e+03
        pdb="HD21 ASN A 359 "    0.005 2.00e-02 2.50e+03
        pdb="HD22 ASN A 359 "   -0.082 2.00e-02 2.50e+03
  ... (remaining 678 not shown)

  Histogram of nonbonded interaction distances:
        1.82 -     2.38: 1978
        2.38 -     2.93: 10703
        2.93 -     3.49: 10615
        3.49 -     4.04: 16031
        4.04 -     4.60: 22249
  Nonbonded interactions: 61576
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 295 "
            pdb=" HZ3 LYS A 311 "
     model   vdw
     1.823 2.450
  nonbonded pdb=" OD2 ASP C 295 "
            pdb=" HZ3 LYS C 311 "
     model   vdw
     1.823 2.450
  nonbonded pdb=" OD2 ASP B 295 "
            pdb=" HZ3 LYS B 311 "
     model   vdw
     1.823 2.450
  nonbonded pdb=" OD1 ASP B 348 "
            pdb=" H   ARG B 349 "
     model   vdw
     1.882 2.450
  nonbonded pdb=" OD1 ASP C 348 "
            pdb=" H   ARG C 349 "
     model   vdw
     1.882 2.450
  ... (remaining 61571 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: 0.02
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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.680
  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:             0.070
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.940
  Find NCS groups from input model:        0.060
  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:12.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
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      :  0.010   0.070   2301  Z= 0.375
  Angle     :  1.272   8.005   3078  Z= 0.672
  Chirality :  0.072   0.244    351
  Planarity :  0.005   0.032    393
  Dihedral  : 11.764  65.195    891
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  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: -2.82 (0.38), residues: 297
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.29), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.018   0.006   HIS B 299 
 PHE   0.011   0.005   PHE B 346 
 TYR   0.015   0.009   TYR A 310 
 ARG   0.005   0.002   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11951 (   48)
  hydrogen bonds       : angle       7.54045 (  144)
  covalent geometry    : bond        0.00957 ( 2301)
  covalent geometry    : angle       1.27163 ( 3078)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  280 LYS cc_start: 0.7089 (tptt) cc_final: 0.6757 (mtpt)
REVERT: B  321 LYS cc_start: 0.7757 (mttt) cc_final: 0.7534 (tttm)
REVERT: B  331 LYS cc_start: 0.8230 (mttt) cc_final: 0.7944 (mttt)
REVERT: B  341 SER cc_start: 0.8365 (m) cc_final: 0.8105 (t)
REVERT: A  294 LYS cc_start: 0.8630 (mttt) cc_final: 0.8257 (mttt)
REVERT: A  353 LYS cc_start: 0.8472 (ttpt) cc_final: 0.8178 (ttmm)
REVERT: A  358 ASP cc_start: 0.7447 (t0) cc_final: 0.7180 (t0)
REVERT: A  372 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7880 (mt-10)
REVERT: C  294 LYS cc_start: 0.8806 (mttt) cc_final: 0.8306 (mtpt)
REVERT: C  316 SER cc_start: 0.8344 (m) cc_final: 0.8006 (p)
REVERT: C  331 LYS cc_start: 0.8428 (mttt) cc_final: 0.8151 (mttp)
REVERT: C  345 ASP cc_start: 0.7381 (m-30) cc_final: 0.7153 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 2.3009
  time to fit residues: 274.5276
Evaluate side-chains
  72 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
B 279 ASN
B 286 ASN
B 336 GLN
C 368 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.152659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.137284 restraints weight = 7726.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.4130 rms_B_bonded: 1.91
r_work: 0.4043 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3950 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.4376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2301  Z= 0.125
  Angle     :  0.606   4.947   3078  Z= 0.309
  Chirality :  0.051   0.137    351
  Planarity :  0.003   0.027    393
  Dihedral  :  6.908  18.448    306
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 15.91 %
    Favored  : 81.06 %
  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: -3.15 (0.36), residues: 297
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.39 (0.28), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B 374 
 PHE   0.003   0.001   PHE C 346 
 TYR   0.004   0.001   TYR C 310 
 ARG   0.001   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02611 (   48)
  hydrogen bonds       : angle       5.90594 (  144)
  covalent geometry    : bond        0.00296 ( 2301)
  covalent geometry    : angle       0.60561 ( 3078)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  341 SER cc_start: 0.8664 (m) cc_final: 0.8357 (t)
REVERT: B  369 LYS cc_start: 0.8002 (mttt) cc_final: 0.7607 (ttmt)
REVERT: A  316 SER cc_start: 0.8877 (m) cc_final: 0.8657 (p)
REVERT: A  349 ARG cc_start: 0.8323 (mtp85) cc_final: 0.8088 (mtp180)
REVERT: A  353 LYS cc_start: 0.8781 (ttpt) cc_final: 0.8540 (ttmm)
REVERT: A  369 LYS cc_start: 0.8362 (mttt) cc_final: 0.7974 (ttmt)
REVERT: C  369 LYS cc_start: 0.8284 (mttt) cc_final: 0.7796 (ttpt)
  outliers start: 8
  outliers final: 2
  residues processed: 76
  average time/residue: 2.0382
  time to fit residues: 158.8091
Evaluate side-chains
  67 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  352 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 2 optimal weight:    0.6980
   chunk 7 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
B 362 HIS
A 362 HIS
C 351 GLN
C 362 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.137765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.124169 restraints weight = 8495.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3986 rms_B_bonded: 1.74
r_work: 0.3904 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3815 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.5387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2301  Z= 0.191
  Angle     :  0.600   5.042   3078  Z= 0.307
  Chirality :  0.051   0.133    351
  Planarity :  0.004   0.026    393
  Dihedral  :  6.580  17.852    306
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 18.56 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.39 (0.36), residues: 297
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.58 (0.27), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 299 
 PHE   0.005   0.001   PHE C 346 
 TYR   0.006   0.001   TYR A 310 
 ARG   0.002   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02434 (   48)
  hydrogen bonds       : angle       5.33839 (  144)
  covalent geometry    : bond        0.00428 ( 2301)
  covalent geometry    : angle       0.59976 ( 3078)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  341 SER cc_start: 0.8698 (m) cc_final: 0.8485 (t)
REVERT: B  345 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7735 (m-30)
REVERT: B  369 LYS cc_start: 0.8128 (mttt) cc_final: 0.7710 (ttmt)
REVERT: A  342 GLU cc_start: 0.7312 (tt0) cc_final: 0.7092 (tt0)
REVERT: A  353 LYS cc_start: 0.8865 (ttpt) cc_final: 0.8650 (ttmm)
REVERT: A  369 LYS cc_start: 0.8452 (mttt) cc_final: 0.8198 (ttmt)
REVERT: C  317 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8736 (tttp)
REVERT: C  342 GLU cc_start: 0.4534 (OUTLIER) cc_final: 0.4085 (pm20)
REVERT: C  369 LYS cc_start: 0.8286 (mttt) cc_final: 0.7891 (ttmt)
  outliers start: 7
  outliers final: 2
  residues processed: 71
  average time/residue: 1.8528
  time to fit residues: 135.1879
Evaluate side-chains
  70 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain C residue  317 LYS
Chi-restraints excluded: chain C residue  342 GLU
Chi-restraints excluded: chain C residue  377 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 10 optimal weight:    0.2980
   chunk 3 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 12 optimal weight:    0.3980
   chunk 7 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.8982

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.146367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.132597 restraints weight = 8306.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.4087 rms_B_bonded: 1.80
r_work: 0.4004 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3912 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.5619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   2301  Z= 0.108
  Angle     :  0.552   4.740   3078  Z= 0.277
  Chirality :  0.051   0.131    351
  Planarity :  0.004   0.024    393
  Dihedral  :  6.001  19.122    306
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 21.59 %
    Favored  : 76.89 %
  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: -3.39 (0.36), residues: 297
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.58 (0.28), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 299 
 PHE   0.006   0.001   PHE C 346 
 TYR   0.004   0.001   TYR A 310 
 ARG   0.002   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01981 (   48)
  hydrogen bonds       : angle       5.01174 (  144)
  covalent geometry    : bond        0.00249 ( 2301)
  covalent geometry    : angle       0.55215 ( 3078)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  336 GLN cc_start: 0.8537 (mt0) cc_final: 0.8177 (mt0)
REVERT: B  341 SER cc_start: 0.8652 (m) cc_final: 0.8431 (t)
REVERT: B  369 LYS cc_start: 0.8157 (mttt) cc_final: 0.7761 (ttmt)
REVERT: A  342 GLU cc_start: 0.7302 (tt0) cc_final: 0.7097 (tt0)
REVERT: A  353 LYS cc_start: 0.8875 (ttpt) cc_final: 0.8672 (ttmm)
REVERT: A  369 LYS cc_start: 0.8492 (mttt) cc_final: 0.8196 (ttmt)
REVERT: C  317 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8625 (tttp)
REVERT: C  336 GLN cc_start: 0.8472 (mt0) cc_final: 0.8087 (mt0)
REVERT: C  369 LYS cc_start: 0.8248 (mttt) cc_final: 0.7839 (ttpt)
  outliers start: 4
  outliers final: 1
  residues processed: 67
  average time/residue: 1.8800
  time to fit residues: 129.3195
Evaluate side-chains
  66 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  317 LYS
Chi-restraints excluded: chain C residue  377 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 1 optimal weight:    0.1980
   chunk 20 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    2.2388

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

Flipped N/Q/H residues before XYZ refinement:
A 286 ASN
C 351 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.139099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.125250 restraints weight = 8736.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3998 rms_B_bonded: 1.81
r_work: 0.3909 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3821 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.5758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   2301  Z= 0.173
  Angle     :  0.564   5.151   3078  Z= 0.287
  Chirality :  0.051   0.131    351
  Planarity :  0.004   0.026    393
  Dihedral  :  6.164  19.492    306
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.32 %
    Favored  : 78.41 %
  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: -3.42 (0.36), residues: 297
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.60 (0.28), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 362 
 PHE   0.005   0.001   PHE C 346 
 TYR   0.005   0.001   TYR A 310 
 ARG   0.002   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01986 (   48)
  hydrogen bonds       : angle       4.89425 (  144)
  covalent geometry    : bond        0.00384 ( 2301)
  covalent geometry    : angle       0.56441 ( 3078)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  343 LYS cc_start: 0.8545 (mttt) cc_final: 0.8313 (tptp)
REVERT: B  369 LYS cc_start: 0.8142 (mttt) cc_final: 0.7747 (ttmt)
REVERT: A  342 GLU cc_start: 0.7422 (tt0) cc_final: 0.7169 (tt0)
REVERT: A  353 LYS cc_start: 0.8843 (ttpt) cc_final: 0.8636 (ttmm)
REVERT: A  369 LYS cc_start: 0.8531 (mttt) cc_final: 0.8232 (ttmt)
REVERT: C  317 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8684 (tttp)
REVERT: C  336 GLN cc_start: 0.8509 (mt0) cc_final: 0.8269 (mt0)
REVERT: C  369 LYS cc_start: 0.8255 (mttt) cc_final: 0.7819 (ttpt)
  outliers start: 6
  outliers final: 2
  residues processed: 66
  average time/residue: 1.9629
  time to fit residues: 132.9002
Evaluate side-chains
  65 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  317 LYS
Chi-restraints excluded: chain C residue  377 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0370
   chunk 6 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    2.2064

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

Flipped N/Q/H residues before XYZ refinement:
B 327 ASN
B 336 GLN
C 351 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.138587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.125033 restraints weight = 8542.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3994 rms_B_bonded: 1.77
r_work: 0.3912 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3822 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.5986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   2301  Z= 0.166
  Angle     :  0.557   5.097   3078  Z= 0.284
  Chirality :  0.050   0.131    351
  Planarity :  0.004   0.028    393
  Dihedral  :  6.105  19.409    306
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 18.18 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.49 (0.36), residues: 297
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.66 (0.28), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 362 
 PHE   0.005   0.001   PHE C 346 
 TYR   0.005   0.001   TYR A 310 
 ARG   0.002   0.001   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01815 (   48)
  hydrogen bonds       : angle       4.80929 (  144)
  covalent geometry    : bond        0.00367 ( 2301)
  covalent geometry    : angle       0.55713 ( 3078)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  369 LYS cc_start: 0.8198 (mttt) cc_final: 0.7867 (ttmt)
REVERT: A  369 LYS cc_start: 0.8515 (mttt) cc_final: 0.8245 (ttmt)
REVERT: C  317 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8672 (tttp)
REVERT: C  336 GLN cc_start: 0.8499 (mt0) cc_final: 0.8268 (mt0)
REVERT: C  369 LYS cc_start: 0.8249 (mttt) cc_final: 0.7855 (ttpt)
  outliers start: 8
  outliers final: 4
  residues processed: 67
  average time/residue: 2.0158
  time to fit residues: 138.3660
Evaluate side-chains
  65 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  317 LYS
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain C residue  317 LYS
Chi-restraints excluded: chain C residue  377 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 28 optimal weight:    3.9990
   chunk 29 optimal weight:    0.3980
   chunk 16 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 20 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   chunk 24 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
C 351 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.138400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.124758 restraints weight = 8659.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3984 rms_B_bonded: 1.78
r_work: 0.3900 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3809 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.6156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2301  Z= 0.173
  Angle     :  0.564   5.185   3078  Z= 0.288
  Chirality :  0.050   0.131    351
  Planarity :  0.004   0.028    393
  Dihedral  :  6.087  19.965    306
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 21.21 %
    Favored  : 76.89 %
  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: -3.51 (0.36), residues: 297
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.67 (0.28), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 362 
 PHE   0.005   0.001   PHE C 346 
 TYR   0.005   0.001   TYR A 310 
 ARG   0.002   0.001   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01811 (   48)
  hydrogen bonds       : angle       4.82757 (  144)
  covalent geometry    : bond        0.00385 ( 2301)
  covalent geometry    : angle       0.56412 ( 3078)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  369 LYS cc_start: 0.8281 (mttt) cc_final: 0.7947 (ttmt)
REVERT: A  369 LYS cc_start: 0.8518 (mttt) cc_final: 0.8253 (ttmt)
REVERT: C  317 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8652 (tttp)
REVERT: C  336 GLN cc_start: 0.8525 (mt0) cc_final: 0.8291 (mt0)
REVERT: C  353 LYS cc_start: 0.9038 (ttmt) cc_final: 0.8811 (ttmm)
REVERT: C  369 LYS cc_start: 0.8281 (mttt) cc_final: 0.7884 (ttpt)
  outliers start: 5
  outliers final: 4
  residues processed: 64
  average time/residue: 2.1201
  time to fit residues: 139.1001
Evaluate side-chains
  65 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  317 LYS
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain C residue  317 LYS
Chi-restraints excluded: chain C residue  377 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   chunk 22 optimal weight:    0.6980
   chunk 20 optimal weight:    6.9990
   chunk 15 optimal weight:    0.6980
   chunk 19 optimal weight:    0.2980
   chunk 2 optimal weight:    0.0270
   chunk 0 optimal weight:    4.9990
   chunk 8 optimal weight:    0.6980
   chunk 29 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0270
   overall best weight:    0.3496

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.148477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.134633 restraints weight = 8248.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.4098 rms_B_bonded: 1.81
r_work: 0.4003 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3912 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.6326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   2301  Z= 0.089
  Angle     :  0.525   5.220   3078  Z= 0.264
  Chirality :  0.051   0.128    351
  Planarity :  0.004   0.029    393
  Dihedral  :  5.487  22.194    306
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 21.59 %
    Favored  : 76.89 %
  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: -3.55 (0.36), residues: 297
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.27), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 299 
 PHE   0.001   0.000   PHE B 346 
 TYR   0.002   0.001   TYR C 310 
 ARG   0.002   0.000   ARG C 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01496 (   48)
  hydrogen bonds       : angle       4.48717 (  144)
  covalent geometry    : bond        0.00219 ( 2301)
  covalent geometry    : angle       0.52516 ( 3078)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  336 GLN cc_start: 0.8546 (mt0) cc_final: 0.8155 (mt0)
REVERT: B  369 LYS cc_start: 0.8252 (mttt) cc_final: 0.7920 (ttmt)
REVERT: A  349 ARG cc_start: 0.8434 (mtp85) cc_final: 0.8211 (mtp180)
REVERT: A  369 LYS cc_start: 0.8363 (mttt) cc_final: 0.8109 (ttmt)
REVERT: C  345 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.8001 (m-30)
REVERT: C  353 LYS cc_start: 0.8997 (ttmt) cc_final: 0.8768 (ttmm)
REVERT: C  369 LYS cc_start: 0.8269 (mttt) cc_final: 0.7828 (tttt)
  outliers start: 4
  outliers final: 1
  residues processed: 70
  average time/residue: 2.5971
  time to fit residues: 186.8553
Evaluate side-chains
  62 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 60
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain C residue  345 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 28 optimal weight:    0.0870
   chunk 8 optimal weight:    0.7980
   chunk 9 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0870
   overall best weight:    0.5136

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
C 336 GLN
C 351 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.148775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.135423 restraints weight = 8157.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.4144 rms_B_bonded: 1.76
r_work: 0.4061 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3976 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.6487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   2301  Z= 0.093
  Angle     :  0.519   4.917   3078  Z= 0.263
  Chirality :  0.051   0.129    351
  Planarity :  0.004   0.028    393
  Dihedral  :  5.345  21.738    306
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 23.86 %
    Favored  : 75.38 %
  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: -3.53 (0.36), residues: 297
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.28), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 299 
 PHE   0.003   0.001   PHE A 346 
 TYR   0.003   0.001   TYR A 310 
 ARG   0.001   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01456 (   48)
  hydrogen bonds       : angle       4.42233 (  144)
  covalent geometry    : bond        0.00229 ( 2301)
  covalent geometry    : angle       0.51902 ( 3078)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  358 ASP cc_start: 0.6907 (t0) cc_final: 0.6681 (t0)
REVERT: B  369 LYS cc_start: 0.8232 (mttt) cc_final: 0.7947 (ttmt)
REVERT: A  349 ARG cc_start: 0.8446 (mtp85) cc_final: 0.8246 (mtt180)
REVERT: A  369 LYS cc_start: 0.8444 (mttt) cc_final: 0.8233 (ttmt)
REVERT: C  353 LYS cc_start: 0.8980 (ttmt) cc_final: 0.8753 (ttmm)
REVERT: C  369 LYS cc_start: 0.8280 (mttt) cc_final: 0.7834 (tttt)
  outliers start: 2
  outliers final: 0
  residues processed: 62
  average time/residue: 1.7444
  time to fit residues: 111.3237
Evaluate side-chains
  57 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 6 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0770
   chunk 29 optimal weight:    6.9990
   chunk 14 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 9 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.7544

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

Flipped N/Q/H residues before XYZ refinement:
C 351 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.140405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.127083 restraints weight = 8497.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.4038 rms_B_bonded: 1.75
r_work: 0.3958 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3870 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.6482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   2301  Z= 0.146
  Angle     :  0.579   7.261   3078  Z= 0.289
  Chirality :  0.050   0.132    351
  Planarity :  0.005   0.065    393
  Dihedral  :  5.700  20.792    306
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 26.14 %
    Favored  : 73.86 %
  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: -3.54 (0.37), residues: 297
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.28), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 362 
 PHE   0.005   0.001   PHE A 346 
 TYR   0.005   0.001   TYR A 310 
 ARG   0.002   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01600 (   48)
  hydrogen bonds       : angle       4.63799 (  144)
  covalent geometry    : bond        0.00342 ( 2301)
  covalent geometry    : angle       0.57904 ( 3078)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  369 LYS cc_start: 0.8247 (mttt) cc_final: 0.7951 (ttmt)
REVERT: C  353 LYS cc_start: 0.9019 (ttmt) cc_final: 0.8813 (ttmm)
REVERT: C  369 LYS cc_start: 0.8316 (mttt) cc_final: 0.7892 (ttpt)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 2.6940
  time to fit residues: 155.1936
Evaluate side-chains
  55 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 29 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 17 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0980
   chunk 11 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    2.0186

-------------------------------------------------------------------------------
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 = 0.4185 r_free = 0.4185 target = 0.138604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.125151 restraints weight = 8602.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3998 rms_B_bonded: 1.75
r_work: 0.3907 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3820 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.6596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2301  Z= 0.158
  Angle     :  0.568   4.989   3078  Z= 0.288
  Chirality :  0.050   0.130    351
  Planarity :  0.005   0.062    393
  Dihedral  :  5.814  20.346    306
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 25.38 %
    Favored  : 73.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.57 (0.36), residues: 297
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.71 (0.28), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 299 
 PHE   0.003   0.001   PHE A 346 
 TYR   0.005   0.001   TYR A 310 
 ARG   0.002   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01616 (   48)
  hydrogen bonds       : angle       4.70548 (  144)
  covalent geometry    : bond        0.00357 ( 2301)
  covalent geometry    : angle       0.56835 ( 3078)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5636.30 seconds
wall clock time: 97 minutes 56.51 seconds (5876.51 seconds total)