Starting phenix.real_space_refine
on Mon Feb 10 21:48:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8otg_17178/02_2025/8otg_17178.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8otg_17178/02_2025/8otg_17178.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8otg_17178/02_2025/8otg_17178.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8otg_17178/02_2025/8otg_17178.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8otg_17178/02_2025/8otg_17178.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8otg_17178/02_2025/8otg_17178.cif"
  }
  resolution = 2.1
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       5      5.16       5
     C    1800      2.51       5
     N     530      2.21       5
     O     535      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 2870
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 2.44, per 1000 atoms: 0.85
  Number of scatterers: 2870
  At special positions: 0
  Unit cell: (123.9, 121.422, 33.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       5     16.00
     O     535      8.00
     N     530      7.00
     C    1800      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.59
  Conformation dependent library (CDL) restraints added in 412.2 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 16 sheets defined
      0.0% alpha, 56.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310
      removed outlier: 6.542A  pdb=" N   GLN A 307 " --> pdb=" O   ILE B 308 " (cutoff:3.500A)
      removed outlier: 7.806A  pdb=" N   TYR B 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   VAL A 309 " --> pdb=" O   TYR B 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314
      removed outlier: 6.758A  pdb=" N   VAL A 313 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 322
      removed outlier: 6.363A  pdb=" N   VAL A 318 " --> pdb=" O   THR E 319 " (cutoff:3.500A)
      removed outlier: 8.272A  pdb=" N   LYS E 321 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   SER A 320 " --> pdb=" O   LYS E 321 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 325 through 330
      removed outlier: 6.828A  pdb=" N   GLY B 326 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   ASN A 327 " --> pdb=" O   GLY B 326 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   GLY A 326 " --> pdb=" O   ASN E 327 " (cutoff:3.500A)
      removed outlier: 8.617A  pdb=" N   HIS E 329 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   ILE A 328 " --> pdb=" O   HIS E 329 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 346
      removed outlier: 6.566A  pdb=" N   GLU A 338 " --> pdb=" O   VAL B 339 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   SER B 341 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   LYS A 340 " --> pdb=" O   SER B 341 " (cutoff:3.500A)
      removed outlier: 8.334A  pdb=" N   LYS B 343 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
      removed outlier: 8.676A  pdb=" N   GLU A 342 " --> pdb=" O   LYS B 343 " (cutoff:3.500A)
      removed outlier: 8.187A  pdb=" N   ASP B 345 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
      removed outlier: 9.132A  pdb=" N   LEU A 344 " --> pdb=" O   ASP B 345 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   LEU E 344 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   ASP A 345 " --> pdb=" O   LEU E 344 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   PHE E 346 " --> pdb=" O   ASP A 345 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 357
      removed outlier: 6.466A  pdb=" N   GLN A 351 " --> pdb=" O   SER B 352 " (cutoff:3.500A)
      removed outlier: 8.124A  pdb=" N   ILE B 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   LYS A 353 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 7.465A  pdb=" N   SER B 356 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   GLY A 355 " --> pdb=" O   SER B 356 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 360 through 362
      removed outlier: 6.316A  pdb=" N   THR A 361 " --> pdb=" O   HIS E 362 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 369 through 378
      removed outlier: 6.635A  pdb=" N   LYS A 369 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
      removed outlier: 8.176A  pdb=" N   GLU B 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ILE A 371 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
      removed outlier: 8.034A  pdb=" N   HIS B 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   THR A 373 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
      removed outlier: 7.978A  pdb=" N   LEU B 376 " --> pdb=" O   THR A 373 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   LYS A 375 " --> pdb=" O   LEU B 376 " (cutoff:3.500A)
      removed outlier: 7.920A  pdb=" N   PHE B 378 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   THR A 377 " --> pdb=" O   PHE B 378 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 306 through 310
    Processing sheet with id=AB1, first strand: chain 'C' and resid 313 through 314
    Processing sheet with id=AB2, first strand: chain 'C' and resid 317 through 322
      removed outlier: 6.364A  pdb=" N   VAL C 318 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 8.273A  pdb=" N   LYS D 321 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   SER C 320 " --> pdb=" O   LYS D 321 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'C' and resid 325 through 330
      removed outlier: 6.219A  pdb=" N   GLY C 326 " --> pdb=" O   ASN D 327 " (cutoff:3.500A)
      removed outlier: 8.617A  pdb=" N   HIS D 329 " --> pdb=" O   GLY C 326 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   ILE C 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'C' and resid 337 through 346
      removed outlier: 6.861A  pdb=" N   LEU D 344 " --> pdb=" O   LYS C 343 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   ASP C 345 " --> pdb=" O   LEU D 344 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   PHE D 346 " --> pdb=" O   ASP C 345 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 350 through 357
    Processing sheet with id=AB6, first strand: chain 'C' and resid 360 through 362
      removed outlier: 6.316A  pdb=" N   THR C 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'C' and resid 369 through 378

    64 hydrogen bonds defined for protein.
    192 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: 0.60

  Time building geometry restraints manager: 0.70 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: 596
        1.34 -     1.46: 644
        1.46 -     1.58: 1670
        1.58 -     1.69: 0
        1.69 -     1.81: 5
  Bond restraints: 2915
  Sorted by residual:
  bond pdb=" C   ARG D 379 "
       pdb=" O   ARG D 379 "
    ideal  model  delta    sigma   weight residual
    1.231  1.338 -0.107 2.00e-02 2.50e+03 2.87e+01
  bond pdb=" C   ARG E 379 "
       pdb=" O   ARG E 379 "
    ideal  model  delta    sigma   weight residual
    1.231  1.338 -0.107 2.00e-02 2.50e+03 2.86e+01
  bond pdb=" C   ARG C 379 "
       pdb=" O   ARG C 379 "
    ideal  model  delta    sigma   weight residual
    1.231  1.338 -0.107 2.00e-02 2.50e+03 2.86e+01
  bond pdb=" C   ARG B 379 "
       pdb=" O   ARG B 379 "
    ideal  model  delta    sigma   weight residual
    1.231  1.337 -0.106 2.00e-02 2.50e+03 2.84e+01
  bond pdb=" C   ARG A 379 "
       pdb=" O   ARG A 379 "
    ideal  model  delta    sigma   weight residual
    1.231  1.337 -0.106 2.00e-02 2.50e+03 2.84e+01
  ... (remaining 2910 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.09: 2822
        1.09 -     2.18: 850
        2.18 -     3.27: 171
        3.27 -     4.36: 47
        4.36 -     5.45: 10
  Bond angle restraints: 3900
  Sorted by residual:
  angle pdb=" CA  ASP D 348 "
        pdb=" CB  ASP D 348 "
        pdb=" CG  ASP D 348 "
      ideal   model   delta    sigma   weight residual
     112.60  116.66   -4.06 1.00e+00 1.00e+00 1.65e+01
  angle pdb=" CA  ASP A 348 "
        pdb=" CB  ASP A 348 "
        pdb=" CG  ASP A 348 "
      ideal   model   delta    sigma   weight residual
     112.60  116.66   -4.06 1.00e+00 1.00e+00 1.64e+01
  angle pdb=" CA  ASP B 348 "
        pdb=" CB  ASP B 348 "
        pdb=" CG  ASP B 348 "
      ideal   model   delta    sigma   weight residual
     112.60  116.66   -4.06 1.00e+00 1.00e+00 1.64e+01
  angle pdb=" CA  ASP C 348 "
        pdb=" CB  ASP C 348 "
        pdb=" CG  ASP C 348 "
      ideal   model   delta    sigma   weight residual
     112.60  116.65   -4.05 1.00e+00 1.00e+00 1.64e+01
  angle pdb=" CA  ASP E 348 "
        pdb=" CB  ASP E 348 "
        pdb=" CG  ASP E 348 "
      ideal   model   delta    sigma   weight residual
     112.60  116.64   -4.04 1.00e+00 1.00e+00 1.63e+01
  ... (remaining 3895 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.04: 1680
       13.04 -    26.08: 50
       26.08 -    39.12: 30
       39.12 -    52.15: 5
       52.15 -    65.19: 15
  Dihedral angle restraints: 1780
    sinusoidal: 745
      harmonic: 1035
  Sorted by residual:
  dihedral pdb=" CA  ILE E 360 "
           pdb=" C   ILE E 360 "
           pdb=" N   THR E 361 "
           pdb=" CA  THR E 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.47   16.53     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  ILE C 360 "
           pdb=" C   ILE C 360 "
           pdb=" N   THR C 361 "
           pdb=" CA  THR C 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.49   16.51     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  ILE A 360 "
           pdb=" C   ILE A 360 "
           pdb=" N   THR A 361 "
           pdb=" CA  THR A 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.51   16.49     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 1777 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 138
       0.034 -    0.068: 115
       0.068 -    0.102: 132
       0.102 -    0.136: 35
       0.136 -    0.170: 20
  Chirality restraints: 440
  Sorted by residual:
  chirality pdb=" CB  ILE C 328 "
            pdb=" CA  ILE C 328 "
            pdb=" CG1 ILE C 328 "
            pdb=" CG2 ILE C 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 7.20e-01
  chirality pdb=" CB  ILE E 328 "
            pdb=" CA  ILE E 328 "
            pdb=" CG1 ILE E 328 "
            pdb=" CG2 ILE E 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 7.04e-01
  chirality pdb=" CB  ILE A 328 "
            pdb=" CA  ILE A 328 "
            pdb=" CG1 ILE A 328 "
            pdb=" CG2 ILE A 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 7.03e-01
  ... (remaining 437 not shown)

  Planarity restraints: 495
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 363 "    0.008 2.00e-02 2.50e+03   1.59e-02 2.51e+00
        pdb=" C   VAL B 363 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   VAL B 363 "    0.010 2.00e-02 2.50e+03
        pdb=" N   PRO B 364 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E 363 "    0.008 2.00e-02 2.50e+03   1.58e-02 2.49e+00
        pdb=" C   VAL E 363 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   VAL E 363 "    0.010 2.00e-02 2.50e+03
        pdb=" N   PRO E 364 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D 363 "   -0.008 2.00e-02 2.50e+03   1.57e-02 2.48e+00
        pdb=" C   VAL D 363 "    0.027 2.00e-02 2.50e+03
        pdb=" O   VAL D 363 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   PRO D 364 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 492 not shown)

  Histogram of nonbonded interaction distances:
        2.48 -     2.96: 1130
        2.96 -     3.45: 2178
        3.45 -     3.93: 4648
        3.93 -     4.42: 4399
        4.42 -     4.90: 8706
  Nonbonded interactions: 21061
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 361 "
            pdb=" ND1 HIS E 330 "
     model   vdw
     2.479 3.120
  nonbonded pdb=" ND1 HIS A 330 "
            pdb=" OG1 THR B 361 "
     model   vdw
     2.479 3.120
  nonbonded pdb=" OG1 THR C 361 "
            pdb=" ND1 HIS D 330 "
     model   vdw
     2.480 3.120
  nonbonded pdb=" N   ASP C 348 "
            pdb=" O   ASP C 348 "
     model   vdw
     2.614 2.496
  nonbonded pdb=" N   ASP A 348 "
            pdb=" O   ASP A 348 "
     model   vdw
     2.614 2.496
  ... (remaining 21056 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'
  selection = chain 'E'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.670
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.710
  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:11.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8816
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      :  0.009   0.107   2915  Z= 0.593
  Angle     :  1.122   5.450   3900  Z= 0.735
  Chirality :  0.072   0.170    440
  Planarity :  0.005   0.027    495
  Dihedral  : 11.339  65.192   1120
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 1.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  :  1.52 %
    Favored  : 95.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.33), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.20 (0.25), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS E 362 
 PHE   0.010   0.003   PHE C 378 
 TYR   0.005   0.004   TYR D 310 
 ARG   0.001   0.000   ARG D 349 

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

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 150
  time to evaluate  : 0.377 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8784 (mttt) cc_final: 0.8553 (mttm)
REVERT: A  379 ARG cc_start: 0.7216 (ptm160) cc_final: 0.6868 (ptp90)
REVERT: B  321 LYS cc_start: 0.8781 (mttt) cc_final: 0.8554 (mttm)
REVERT: C  321 LYS cc_start: 0.8778 (mttt) cc_final: 0.8506 (mttm)
REVERT: C  340 LYS cc_start: 0.8646 (mtpm) cc_final: 0.8322 (tttp)
REVERT: C  375 LYS cc_start: 0.8594 (tttt) cc_final: 0.8361 (ttmm)
REVERT: C  379 ARG cc_start: 0.7295 (ptm160) cc_final: 0.6650 (ppt90)
REVERT: D  349 ARG cc_start: 0.8600 (mtt180) cc_final: 0.7428 (mmp-170)
REVERT: D  375 LYS cc_start: 0.8491 (tttt) cc_final: 0.8187 (ttmm)
REVERT: E  349 ARG cc_start: 0.8595 (mtt180) cc_final: 0.7470 (mmp-170)
REVERT: E  375 LYS cc_start: 0.8481 (tttt) cc_final: 0.8240 (ttmm)
  outliers start: 10
  outliers final: 0
  residues processed: 160
  average time/residue: 1.4625
  time to fit residues: 238.1567
Evaluate side-chains
  83 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 29 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 17 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 31 optimal weight:    9.9990
   chunk 21 optimal weight:    8.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 351 GLN
B 307 GLN
B 327 ASN
B 351 GLN
C 307 GLN
C 327 ASN
C 330 HIS
C 351 GLN
D 307 GLN
D 351 GLN
E 307 GLN
E 351 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.128901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.112396 restraints weight = 3110.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 1.31
r_work: 0.3583 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.3504 rms_B_bonded: 2.46 restraints_weight: 0.2500
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8988
moved from start:          0.3043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2915  Z= 0.205
  Angle     :  0.600   6.184   3900  Z= 0.290
  Chirality :  0.049   0.136    440
  Planarity :  0.003   0.023    495
  Dihedral  :  4.767  13.692    385
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.79 %
    Favored  : 79.39 %
  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: -2.44 (0.34), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.26), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 374 
 PHE   0.018   0.002   PHE E 378 
 TYR   0.008   0.002   TYR C 310 
 ARG   0.004   0.001   ARG E 379 

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

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.372 
Fit side-chains
REVERT: B  379 ARG cc_start: 0.7459 (ptp-110) cc_final: 0.6695 (ptt-90)
REVERT: D  349 ARG cc_start: 0.8596 (mtt180) cc_final: 0.7075 (mmp-170)
REVERT: E  325 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8403 (tt)
REVERT: E  349 ARG cc_start: 0.8619 (mtt180) cc_final: 0.7323 (mmp-170)
  outliers start: 6
  outliers final: 3
  residues processed: 88
  average time/residue: 1.3742
  time to fit residues: 123.4453
Evaluate side-chains
  86 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain B residue  317 LYS
Chi-restraints excluded: chain C residue  317 LYS
Chi-restraints excluded: chain E residue  325 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 25 optimal weight:    0.0870
   chunk 34 optimal weight:    0.5980
   chunk 22 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   chunk 32 optimal weight:    0.2980
   chunk 30 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 28 optimal weight:    6.9990
   overall best weight:    0.5960

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
B 307 GLN
C 307 GLN
D 307 GLN
D 351 GLN
E 307 GLN
E 351 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.133589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.117556 restraints weight = 3072.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3756 rms_B_bonded: 1.31
r_work: 0.3663 rms_B_bonded: 1.48 restraints_weight: 0.5000
r_work: 0.3586 rms_B_bonded: 2.49 restraints_weight: 0.2500
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8944
moved from start:          0.3341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   2915  Z= 0.114
  Angle     :  0.495   5.284   3900  Z= 0.242
  Chirality :  0.048   0.126    440
  Planarity :  0.003   0.018    495
  Dihedral  :  4.284  11.899    385
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 1.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.79 %
    Favored  : 79.39 %
  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: -2.27 (0.34), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.72 (0.26), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A 374 
 PHE   0.013   0.002   PHE E 378 
 TYR   0.009   0.002   TYR C 310 
 ARG   0.004   0.000   ARG D 379 

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

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.342 
Fit side-chains
REVERT: D  349 ARG cc_start: 0.8575 (mtt180) cc_final: 0.7078 (mmp-170)
REVERT: E  325 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.7988 (tt)
REVERT: E  349 ARG cc_start: 0.8598 (mtt180) cc_final: 0.7080 (mmp-170)
  outliers start: 6
  outliers final: 1
  residues processed: 90
  average time/residue: 1.3916
  time to fit residues: 128.0727
Evaluate side-chains
  84 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 82
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain E residue  325 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    8.9990
   chunk 19 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   chunk 11 optimal weight:    0.0980
   chunk 34 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   overall best weight:    2.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
B 307 GLN
C 307 GLN
C 351 GLN
D 307 GLN
D 351 GLN
E 307 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.126689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.109954 restraints weight = 3137.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 1.33
r_work: 0.3537 rms_B_bonded: 1.48 restraints_weight: 0.5000
r_work: 0.3457 rms_B_bonded: 2.47 restraints_weight: 0.2500
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9022
moved from start:          0.3302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2915  Z= 0.254
  Angle     :  0.598   6.760   3900  Z= 0.298
  Chirality :  0.050   0.135    440
  Planarity :  0.003   0.017    495
  Dihedral  :  4.832  14.287    385
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 19.70 %
    Favored  : 79.39 %
  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: -2.21 (0.33), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.68 (0.25), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 329 
 PHE   0.012   0.002   PHE B 378 
 TYR   0.007   0.002   TYR E 310 
 ARG   0.003   0.000   ARG B 379 

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

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 0.377 
Fit side-chains
REVERT: D  325 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8566 (tt)
REVERT: D  349 ARG cc_start: 0.8634 (mtt180) cc_final: 0.7241 (mmp-170)
REVERT: E  325 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8708 (tt)
REVERT: E  349 ARG cc_start: 0.8600 (mtt180) cc_final: 0.7113 (mmp-170)
REVERT: E  379 ARG cc_start: 0.5537 (OUTLIER) cc_final: 0.4521 (mtt-85)
  outliers start: 3
  outliers final: 0
  residues processed: 85
  average time/residue: 1.3360
  time to fit residues: 116.0548
Evaluate side-chains
  83 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  379 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 7 optimal weight:    8.9990
   chunk 14 optimal weight:    8.9990
   chunk 15 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   chunk 4 optimal weight:   10.0000
   chunk 26 optimal weight:    0.0770
   chunk 34 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 8 optimal weight:    9.9990
   overall best weight:    4.0146

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
B 307 GLN
C 307 GLN
C 351 GLN
D 307 GLN
D 327 ASN
E 307 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.126055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.109280 restraints weight = 3105.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 1.33
r_work: 0.3527 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.3445 rms_B_bonded: 2.45 restraints_weight: 0.2500
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9044
moved from start:          0.3438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   2915  Z= 0.381
  Angle     :  0.682   8.184   3900  Z= 0.342
  Chirality :  0.052   0.144    440
  Planarity :  0.003   0.016    495
  Dihedral  :  5.177  15.831    385
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 19.09 %
    Favored  : 79.09 %
  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: -2.09 (0.33), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.59 (0.25), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 330 
 PHE   0.012   0.002   PHE C 378 
 TYR   0.009   0.002   TYR E 310 
 ARG   0.002   0.000   ARG D 379 

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

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.375 
Fit side-chains
REVERT: C  317 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8499 (mttm)
REVERT: D  349 ARG cc_start: 0.8638 (mtt180) cc_final: 0.7211 (mmp-170)
REVERT: E  325 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8833 (tt)
REVERT: E  349 ARG cc_start: 0.8665 (mtt180) cc_final: 0.7291 (mmp-170)
REVERT: E  379 ARG cc_start: 0.5393 (OUTLIER) cc_final: 0.4315 (mtt-85)
  outliers start: 6
  outliers final: 1
  residues processed: 87
  average time/residue: 1.4129
  time to fit residues: 125.5288
Evaluate side-chains
  84 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 ARG
Chi-restraints excluded: chain C residue  317 LYS
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  379 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:    8.9990
   chunk 4 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 327 ASN
A 351 GLN
B 307 GLN
C 307 GLN
C 351 GLN
D 307 GLN
D 351 GLN
E 307 GLN
E 351 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.126231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.109436 restraints weight = 3131.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 1.33
r_work: 0.3527 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.3445 rms_B_bonded: 2.45 restraints_weight: 0.2500
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9047
moved from start:          0.3524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   2915  Z= 0.379
  Angle     :  0.673   8.872   3900  Z= 0.340
  Chirality :  0.052   0.142    440
  Planarity :  0.003   0.016    495
  Dihedral  :  5.242  15.948    385
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.58 %
    Favored  : 79.70 %
  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: -1.96 (0.33), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.48 (0.25), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 329 
 PHE   0.011   0.002   PHE C 378 
 TYR   0.010   0.002   TYR E 310 
 ARG   0.002   0.000   ARG D 379 

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

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.362 
Fit side-chains
REVERT: B  317 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8645 (mttp)
REVERT: C  317 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8506 (mttm)
REVERT: D  349 ARG cc_start: 0.8646 (mtt180) cc_final: 0.7220 (mmp-170)
REVERT: E  325 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8805 (tt)
REVERT: E  349 ARG cc_start: 0.8670 (mtt180) cc_final: 0.7299 (mmp-170)
REVERT: E  379 ARG cc_start: 0.5461 (OUTLIER) cc_final: 0.4341 (mtt-85)
  outliers start: 9
  outliers final: 1
  residues processed: 90
  average time/residue: 1.3695
  time to fit residues: 125.8441
Evaluate side-chains
  87 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 ARG
Chi-restraints excluded: chain B residue  317 LYS
Chi-restraints excluded: chain C residue  317 LYS
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  379 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 17 optimal weight:    0.6980
   chunk 7 optimal weight:    8.9990
   chunk 0 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 4 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
B 307 GLN
C 307 GLN
C 351 GLN
D 307 GLN
D 351 GLN
E 307 GLN
E 351 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.129706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.113271 restraints weight = 3168.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3686 rms_B_bonded: 1.33
r_work: 0.3586 rms_B_bonded: 1.48 restraints_weight: 0.5000
r_work: 0.3506 rms_B_bonded: 2.49 restraints_weight: 0.2500
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9010
moved from start:          0.3592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   2915  Z= 0.171
  Angle     :  0.596   8.958   3900  Z= 0.289
  Chirality :  0.049   0.129    440
  Planarity :  0.002   0.013    495
  Dihedral  :  4.844  14.541    385
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 20.00 %
    Favored  : 78.48 %
  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: -1.86 (0.34), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.41 (0.26), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS A 374 
 PHE   0.009   0.002   PHE C 378 
 TYR   0.011   0.002   TYR D 310 
 ARG   0.002   0.000   ARG D 379 

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

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.346 
Fit side-chains
REVERT: D  349 ARG cc_start: 0.8644 (mtt180) cc_final: 0.7246 (mmp-170)
REVERT: D  379 ARG cc_start: 0.5622 (OUTLIER) cc_final: 0.4623 (mtt-85)
REVERT: E  325 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8414 (tt)
REVERT: E  349 ARG cc_start: 0.8671 (mtt180) cc_final: 0.7156 (mmp-170)
REVERT: E  379 ARG cc_start: 0.5313 (OUTLIER) cc_final: 0.4212 (mtt-85)
  outliers start: 5
  outliers final: 1
  residues processed: 84
  average time/residue: 1.4012
  time to fit residues: 120.1863
Evaluate side-chains
  84 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  331 LYS
Chi-restraints excluded: chain D residue  379 ARG
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  379 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 32 optimal weight:    7.9990
   chunk 2 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0870
   chunk 11 optimal weight:    0.0060
   chunk 28 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 24 optimal weight:   20.0000
   overall best weight:    1.5578

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
B 307 GLN
C 307 GLN
C 351 GLN
D 307 GLN
D 351 GLN
E 307 GLN
E 351 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.126523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.109875 restraints weight = 3178.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3673 rms_B_bonded: 1.34
r_work: 0.3569 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.3489 rms_B_bonded: 2.50 restraints_weight: 0.2500
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9011
moved from start:          0.3624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2915  Z= 0.179
  Angle     :  0.591   8.741   3900  Z= 0.293
  Chirality :  0.049   0.130    440
  Planarity :  0.002   0.013    495
  Dihedral  :  4.784  14.235    385
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 19.39 %
    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: -1.78 (0.34), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.35 (0.26), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A 374 
 PHE   0.009   0.002   PHE C 378 
 TYR   0.011   0.002   TYR E 310 
 ARG   0.002   0.000   ARG D 379 

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

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.392 
Fit side-chains
REVERT: D  325 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8556 (tt)
REVERT: D  349 ARG cc_start: 0.8678 (mtt180) cc_final: 0.7279 (mmp-170)
REVERT: D  379 ARG cc_start: 0.5669 (OUTLIER) cc_final: 0.4662 (mtt-85)
REVERT: E  325 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8459 (tt)
REVERT: E  349 ARG cc_start: 0.8685 (mtt180) cc_final: 0.7173 (mmp-170)
REVERT: E  379 ARG cc_start: 0.5436 (OUTLIER) cc_final: 0.4346 (mtt-85)
  outliers start: 6
  outliers final: 1
  residues processed: 85
  average time/residue: 1.3781
  time to fit residues: 119.6221
Evaluate side-chains
  86 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  331 LYS
Chi-restraints excluded: chain D residue  379 ARG
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  379 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 14 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   chunk 4 optimal weight:    9.9990
   chunk 32 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 16 optimal weight:   10.0000
   chunk 26 optimal weight:    7.9990
   chunk 34 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
B 307 GLN
C 307 GLN
C 351 GLN
D 307 GLN
D 351 GLN
E 307 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.123929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.107068 restraints weight = 3148.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 1.32
r_work: 0.3525 rms_B_bonded: 1.48 restraints_weight: 0.5000
r_work: 0.3442 rms_B_bonded: 2.46 restraints_weight: 0.2500
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9034
moved from start:          0.3579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   2915  Z= 0.298
  Angle     :  0.678   8.861   3900  Z= 0.336
  Chirality :  0.051   0.139    440
  Planarity :  0.002   0.014    495
  Dihedral  :  5.065  15.008    385
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 20.00 %
    Favored  : 78.48 %
  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: -1.79 (0.34), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.35 (0.26), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D 329 
 PHE   0.009   0.002   PHE C 378 
 TYR   0.010   0.002   TYR E 310 
 ARG   0.002   0.000   ARG D 379 

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

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.362 
Fit side-chains
REVERT: D  325 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8762 (tt)
REVERT: D  349 ARG cc_start: 0.8673 (mtt180) cc_final: 0.7264 (mmp-170)
REVERT: D  379 ARG cc_start: 0.5620 (OUTLIER) cc_final: 0.4609 (mtt-85)
REVERT: E  325 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8737 (tt)
REVERT: E  349 ARG cc_start: 0.8647 (mtt180) cc_final: 0.7319 (mmp-170)
REVERT: E  379 ARG cc_start: 0.5454 (OUTLIER) cc_final: 0.4348 (mtt-85)
  outliers start: 5
  outliers final: 0
  residues processed: 84
  average time/residue: 1.3942
  time to fit residues: 119.6484
Evaluate side-chains
  85 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  379 ARG
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  379 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   chunk 2 optimal weight:    6.9990
   chunk 23 optimal weight:    9.9990
   chunk 10 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 24 optimal weight:   10.0000
   chunk 29 optimal weight:   10.0000
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
B 307 GLN
C 307 GLN
C 351 GLN
D 307 GLN
D 351 GLN
E 307 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.123157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.106207 restraints weight = 3180.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 1.33
r_work: 0.3511 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.3428 rms_B_bonded: 2.47 restraints_weight: 0.2500
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9043
moved from start:          0.3597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   2915  Z= 0.366
  Angle     :  0.709   8.811   3900  Z= 0.360
  Chirality :  0.052   0.141    440
  Planarity :  0.003   0.015    495
  Dihedral  :  5.214  15.622    385
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 20.00 %
    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: -1.78 (0.34), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.35 (0.26), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 329 
 PHE   0.010   0.002   PHE C 378 
 TYR   0.009   0.002   TYR E 310 
 ARG   0.001   0.000   ARG D 379 

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

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.338 
Fit side-chains
REVERT: D  349 ARG cc_start: 0.8672 (mtt180) cc_final: 0.7264 (mmp-170)
REVERT: D  379 ARG cc_start: 0.5556 (OUTLIER) cc_final: 0.5110 (mtt-85)
REVERT: E  325 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8790 (tt)
REVERT: E  349 ARG cc_start: 0.8665 (mtt180) cc_final: 0.7319 (mmp-170)
REVERT: E  379 ARG cc_start: 0.5539 (OUTLIER) cc_final: 0.4383 (mtt-85)
  outliers start: 4
  outliers final: 0
  residues processed: 84
  average time/residue: 1.3805
  time to fit residues: 118.4368
Evaluate side-chains
  85 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 82
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  379 ARG
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  379 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 23 optimal weight:    8.9990
   chunk 12 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0670
   chunk 31 optimal weight:    0.8980
   chunk 7 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   chunk 34 optimal weight:    6.9990
   chunk 14 optimal weight:    8.9990
   overall best weight:    2.9924

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
B 307 GLN
C 307 GLN
D 307 GLN
D 351 GLN
E 307 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.123933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.107121 restraints weight = 3096.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 1.31
r_work: 0.3525 rms_B_bonded: 1.48 restraints_weight: 0.5000
r_work: 0.3443 rms_B_bonded: 2.45 restraints_weight: 0.2500
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9033
moved from start:          0.3596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2915  Z= 0.302
  Angle     :  0.705   9.490   3900  Z= 0.351
  Chirality :  0.051   0.137    440
  Planarity :  0.002   0.014    495
  Dihedral  :  5.151  15.490    385
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 19.70 %
    Favored  : 79.09 %
  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: -1.76 (0.34), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.33 (0.26), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D 329 
 PHE   0.009   0.002   PHE C 378 
 TYR   0.010   0.002   TYR D 310 
 ARG   0.002   0.000   ARG D 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3907.75 seconds
wall clock time: 69 minutes 48.64 seconds (4188.64 seconds total)