Starting phenix.real_space_refine
on Fri Aug 22 13:01:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8otg_17178/08_2025/8otg_17178.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8otg_17178/08_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_17178/08_2025/8otg_17178.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8otg_17178/08_2025/8otg_17178.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8otg_17178/08_2025/8otg_17178.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8otg_17178/08_2025/8otg_17178.cif"
  }
  resolution = 2.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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:
    B, C, D, E
  Time building chain proxies: 0.76, per 1000 atoms: 0.26
  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: 0.20
  Conformation dependent library (CDL) restraints added in 87.0 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.12
  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: 0.39

  Time building geometry restraints manager: 0.28 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             4.810
  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:          0.060
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     4.480
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.960
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.90 (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
 ARG   0.001   0.000   ARG D 349 
 TYR   0.005   0.004   TYR D 310 
 PHE   0.010   0.003   PHE C 378 
 HIS   0.005   0.002   HIS E 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00922 ( 2915)
  covalent geometry    : angle       1.12208 ( 3900)
  hydrogen bonds       : bond        0.08488 (   64)
  hydrogen bonds       : angle       5.98049 (  192)

*********************** 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  : 0.153 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8784 (mttt) cc_final: 0.8553 (mttm)
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: 0.6975
  time to fit residues: 113.5014
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  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   chunk 31 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 13 optimal weight:    7.9990
   overall best weight:    1.7784

-------------------------------------------------------------------------------
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 = 0.3959 r_free = 0.3959 target = 0.129240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.112475 restraints weight = 3140.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 1.35
r_work: 0.3582 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3503 rms_B_bonded: 2.51 restraints_weight: 0.2500
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8992
moved from start:          0.3091

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= 0.117
  Angle     :  0.605   6.163   3900  Z= 0.292
  Chirality :  0.049   0.141    440
  Planarity :  0.004   0.024    495
  Dihedral  :  4.776  13.740    385
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 18.79 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.44 (0.34), 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
 ARG   0.004   0.000   ARG E 379 
 TYR   0.007   0.002   TYR C 310 
 PHE   0.018   0.002   PHE E 378 
 HIS   0.002   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 2915)
  covalent geometry    : angle       0.60535 ( 3900)
  hydrogen bonds       : bond        0.02170 (   64)
  hydrogen bonds       : angle       4.91104 (  192)

*********************** 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
  89 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.135 
Fit side-chains
REVERT: B  379 ARG cc_start: 0.7484 (ptp-110) cc_final: 0.6665 (ptt90)
REVERT: D  349 ARG cc_start: 0.8602 (mtt180) cc_final: 0.7072 (mmp-170)
REVERT: E  325 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8393 (tt)
REVERT: E  349 ARG cc_start: 0.8622 (mtt180) cc_final: 0.7316 (mmp-170)
  outliers start: 7
  outliers final: 3
  residues processed: 89
  average time/residue: 0.6347
  time to fit residues: 57.6029
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  : 0.121 
-------------------------------------------------------------------------------
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 9 optimal weight:    0.8980
   chunk 22 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   chunk 19 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 8 optimal weight:    8.9990
   chunk 1 optimal weight:    5.9990
   chunk 30 optimal weight:    8.9990
   chunk 12 optimal weight:    6.9990
   chunk 25 optimal weight:   10.0000
   overall best weight:    3.9788

-------------------------------------------------------------------------------
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 = 0.3896 r_free = 0.3896 target = 0.124981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.108220 restraints weight = 3133.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 1.32
r_work: 0.3512 rms_B_bonded: 1.46 restraints_weight: 0.5000
r_work: 0.3431 rms_B_bonded: 2.44 restraints_weight: 0.2500
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9040
moved from start:          0.3283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   2915  Z= 0.217
  Angle     :  0.668   5.845   3900  Z= 0.337
  Chirality :  0.052   0.145    440
  Planarity :  0.003   0.022    495
  Dihedral  :  5.181  15.017    385
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.88 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.27 (0.32), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.72 (0.25), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 379 
 TYR   0.007   0.002   TYR E 310 
 PHE   0.015   0.002   PHE C 378 
 HIS   0.004   0.001   HIS D 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 ( 2915)
  covalent geometry    : angle       0.66783 ( 3900)
  hydrogen bonds       : bond        0.02772 (   64)
  hydrogen bonds       : angle       5.13518 (  192)

*********************** 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  : 0.086 
Fit side-chains
REVERT: B  379 ARG cc_start: 0.7662 (ptp-110) cc_final: 0.7447 (mtp85)
REVERT: D  349 ARG cc_start: 0.8640 (mtt180) cc_final: 0.7240 (mmp-170)
REVERT: E  325 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8828 (tt)
REVERT: E  349 ARG cc_start: 0.8634 (mtt180) cc_final: 0.7311 (mmp-170)
REVERT: E  379 ARG cc_start: 0.5484 (OUTLIER) cc_final: 0.4380 (mtt-85)
  outliers start: 6
  outliers final: 3
  residues processed: 88
  average time/residue: 0.6200
  time to fit residues: 55.6269
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  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 ARG
Chi-restraints excluded: chain B residue  317 LYS
Chi-restraints excluded: chain D residue  331 LYS
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  379 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 6 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9990
   chunk 3 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    0.5980
   chunk 33 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 4 optimal weight:    9.9990
   chunk 21 optimal weight:    7.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    2.8786

-------------------------------------------------------------------------------
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 327 ASN
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 = 0.3906 r_free = 0.3906 target = 0.125848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.109185 restraints weight = 3103.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 1.31
r_work: 0.3527 rms_B_bonded: 1.46 restraints_weight: 0.5000
r_work: 0.3446 rms_B_bonded: 2.43 restraints_weight: 0.2500
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9032
moved from start:          0.3442

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= 0.163
  Angle     :  0.640   8.005   3900  Z= 0.315
  Chirality :  0.051   0.138    440
  Planarity :  0.003   0.014    495
  Dihedral  :  5.112  15.215    385
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 1.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 18.48 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.11 (0.33), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.60 (0.25), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 379 
 TYR   0.010   0.002   TYR E 310 
 PHE   0.012   0.002   PHE C 378 
 HIS   0.002   0.001   HIS D 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 2915)
  covalent geometry    : angle       0.63972 ( 3900)
  hydrogen bonds       : bond        0.02427 (   64)
  hydrogen bonds       : angle       5.00567 (  192)

*********************** 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
  90 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.111 
Fit side-chains
REVERT: B  379 ARG cc_start: 0.7671 (ptp-110) cc_final: 0.7457 (mtp85)
REVERT: D  349 ARG cc_start: 0.8624 (mtt180) cc_final: 0.7241 (mmp-170)
REVERT: E  325 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8735 (tt)
REVERT: E  349 ARG cc_start: 0.8630 (mtt180) cc_final: 0.7279 (mmp-170)
REVERT: E  379 ARG cc_start: 0.5493 (OUTLIER) cc_final: 0.4367 (mtt-85)
  outliers start: 7
  outliers final: 2
  residues processed: 88
  average time/residue: 0.5820
  time to fit residues: 52.3100
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  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 ARG
Chi-restraints excluded: chain B residue  317 LYS
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  379 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 10 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 21 optimal weight:    8.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:    2.7388

-------------------------------------------------------------------------------
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
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 = 0.3908 r_free = 0.3908 target = 0.125799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.109185 restraints weight = 3085.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 1.30
r_work: 0.3530 rms_B_bonded: 1.46 restraints_weight: 0.5000
r_work: 0.3449 rms_B_bonded: 2.43 restraints_weight: 0.2500
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9032
moved from start:          0.3410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2915  Z= 0.157
  Angle     :  0.624   8.401   3900  Z= 0.310
  Chirality :  0.050   0.136    440
  Planarity :  0.002   0.015    495
  Dihedral  :  5.114  15.261    385
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 1.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 18.18 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.00 (0.33), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.51 (0.25), residues: 365

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 2915)
  covalent geometry    : angle       0.62386 ( 3900)
  hydrogen bonds       : bond        0.02349 (   64)
  hydrogen bonds       : angle       4.94452 (  192)

*********************** 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
  90 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.134 
Fit side-chains
REVERT: B  379 ARG cc_start: 0.7660 (ptp-110) cc_final: 0.7455 (mtp85)
REVERT: C  317 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8477 (mttm)
REVERT: D  325 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8681 (tt)
REVERT: D  349 ARG cc_start: 0.8641 (mtt180) cc_final: 0.7244 (mmp-170)
REVERT: D  379 ARG cc_start: 0.5580 (OUTLIER) cc_final: 0.4591 (mtt-85)
REVERT: E  325 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8701 (tt)
REVERT: E  349 ARG cc_start: 0.8622 (mtt180) cc_final: 0.7300 (mmp-170)
REVERT: E  379 ARG cc_start: 0.5430 (OUTLIER) cc_final: 0.4267 (mtt-85)
  outliers start: 7
  outliers final: 3
  residues processed: 87
  average time/residue: 0.6486
  time to fit residues: 57.5102
Evaluate side-chains
  90 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 ARG
Chi-restraints excluded: chain B residue  317 LYS
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 21 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 11 optimal weight:   10.0000
   chunk 9 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 15 optimal weight:    9.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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
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 = 0.3950 r_free = 0.3950 target = 0.128888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.112573 restraints weight = 3106.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 1.30
r_work: 0.3586 rms_B_bonded: 1.46 restraints_weight: 0.5000
r_work: 0.3506 rms_B_bonded: 2.46 restraints_weight: 0.2500
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9002
moved from start:          0.3559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   2915  Z= 0.093
  Angle     :  0.576   8.573   3900  Z= 0.277
  Chirality :  0.049   0.129    440
  Planarity :  0.002   0.014    495
  Dihedral  :  4.794  14.022    385
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 1.54
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.89 (0.34), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.43 (0.26), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 379 
 TYR   0.011   0.002   TYR D 310 
 PHE   0.009   0.002   PHE C 378 
 HIS   0.001   0.000   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 2915)
  covalent geometry    : angle       0.57599 ( 3900)
  hydrogen bonds       : bond        0.01782 (   64)
  hydrogen bonds       : angle       4.59181 (  192)

*********************** 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
  91 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.135 
Fit side-chains
REVERT: C  317 LYS cc_start: 0.8762 (mtmt) cc_final: 0.8453 (mttm)
REVERT: D  349 ARG cc_start: 0.8646 (mtt180) cc_final: 0.7276 (mmp-170)
REVERT: E  325 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8333 (tt)
REVERT: E  349 ARG cc_start: 0.8640 (mtt180) cc_final: 0.7146 (mmp-170)
  outliers start: 5
  outliers final: 1
  residues processed: 90
  average time/residue: 0.5984
  time to fit residues: 54.9499
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  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  331 LYS
Chi-restraints excluded: chain E residue  325 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 21 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   chunk 23 optimal weight:   10.0000
   chunk 8 optimal weight:    8.9990
   chunk 25 optimal weight:    8.9990
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    7.9990
   chunk 3 optimal weight:    8.9990
   chunk 20 optimal weight:    0.7980
   chunk 32 optimal weight:    7.9990
   overall best weight:    4.5588

-------------------------------------------------------------------------------
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
B 330 HIS
C 307 GLN
C 351 GLN
D 307 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 = 0.3884 r_free = 0.3884 target = 0.123863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.107128 restraints weight = 3104.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 1.30
r_work: 0.3500 rms_B_bonded: 1.46 restraints_weight: 0.5000
r_work: 0.3417 rms_B_bonded: 2.43 restraints_weight: 0.2500
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9053
moved from start:          0.3445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   2915  Z= 0.248
  Angle     :  0.696   8.408   3900  Z= 0.352
  Chirality :  0.053   0.145    440
  Planarity :  0.003   0.018    495
  Dihedral  :  5.326  16.147    385
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 19.09 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.85 (0.33), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.40 (0.25), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 379 
 TYR   0.010   0.002   TYR E 310 
 PHE   0.010   0.002   PHE C 378 
 HIS   0.003   0.001   HIS D 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00604 ( 2915)
  covalent geometry    : angle       0.69563 ( 3900)
  hydrogen bonds       : bond        0.02833 (   64)
  hydrogen bonds       : angle       5.11332 (  192)

*********************** 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
  89 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.158 
Fit side-chains
REVERT: B  379 ARG cc_start: 0.7622 (mtp85) cc_final: 0.7324 (mtt-85)
REVERT: C  317 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8497 (mttm)
REVERT: D  349 ARG cc_start: 0.8667 (mtt180) cc_final: 0.7264 (mmp-170)
REVERT: D  379 ARG cc_start: 0.5531 (OUTLIER) cc_final: 0.5189 (mtt-85)
REVERT: E  325 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8923 (tt)
REVERT: E  349 ARG cc_start: 0.8603 (mtt180) cc_final: 0.7322 (mmp-170)
REVERT: E  379 ARG cc_start: 0.5491 (OUTLIER) cc_final: 0.5246 (mtt-85)
  outliers start: 5
  outliers final: 2
  residues processed: 86
  average time/residue: 0.6324
  time to fit residues: 55.3933
Evaluate side-chains
  88 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 ARG
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 34 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 13 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 7 optimal weight:    0.4980
   chunk 20 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   chunk 5 optimal weight:   10.0000
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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
E 307 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.129834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.113803 restraints weight = 3165.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3702 rms_B_bonded: 1.31
r_work: 0.3604 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.3525 rms_B_bonded: 2.47 restraints_weight: 0.2500
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8992
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      :  0.002   0.020   2915  Z= 0.082
  Angle     :  0.573   8.888   3900  Z= 0.276
  Chirality :  0.049   0.126    440
  Planarity :  0.002   0.014    495
  Dihedral  :  4.726  13.850    385
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 1.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 19.09 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.74 (0.34), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.32 (0.26), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 379 
 TYR   0.011   0.003   TYR D 310 
 PHE   0.009   0.001   PHE C 378 
 HIS   0.001   0.000   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00193 ( 2915)
  covalent geometry    : angle       0.57278 ( 3900)
  hydrogen bonds       : bond        0.01620 (   64)
  hydrogen bonds       : angle       4.43227 (  192)

*********************** 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
  91 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.132 
Fit side-chains
REVERT: C  317 LYS cc_start: 0.8746 (mtmt) cc_final: 0.8429 (mttm)
REVERT: D  325 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8389 (tt)
REVERT: D  349 ARG cc_start: 0.8657 (mtt180) cc_final: 0.7300 (mmp-170)
REVERT: D  379 ARG cc_start: 0.5576 (OUTLIER) cc_final: 0.5171 (mtt-85)
REVERT: E  325 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8204 (tt)
REVERT: E  349 ARG cc_start: 0.8637 (mtt180) cc_final: 0.7164 (mmp-170)
REVERT: E  379 ARG cc_start: 0.5639 (OUTLIER) cc_final: 0.4573 (mtt-85)
  outliers start: 5
  outliers final: 1
  residues processed: 89
  average time/residue: 0.6179
  time to fit residues: 56.1016
Evaluate side-chains
  88 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
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 32 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 23 optimal weight:    9.9990
   chunk 2 optimal weight:    9.9990
   chunk 24 optimal weight:    2.9990
   chunk 14 optimal weight:    8.9990
   chunk 1 optimal weight:    8.9990
   chunk 17 optimal weight:    4.9990
   chunk 10 optimal weight:    9.9990
   chunk 27 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    2.5588

-------------------------------------------------------------------------------
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 = 0.126094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.109481 restraints weight = 3155.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 1.31
r_work: 0.3534 rms_B_bonded: 1.46 restraints_weight: 0.5000
r_work: 0.3454 rms_B_bonded: 2.44 restraints_weight: 0.2500
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9030
moved from start:          0.3526

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= 0.151
  Angle     :  0.642   8.834   3900  Z= 0.321
  Chirality :  0.050   0.136    440
  Planarity :  0.002   0.013    495
  Dihedral  :  5.033  14.584    385
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 1.71
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.73 (0.34), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.31 (0.26), residues: 365

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 2915)
  covalent geometry    : angle       0.64216 ( 3900)
  hydrogen bonds       : bond        0.02222 (   64)
  hydrogen bonds       : angle       4.67622 (  192)

*********************** 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
  88 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.131 
Fit side-chains
REVERT: C  317 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8451 (mttm)
REVERT: D  325 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8745 (tt)
REVERT: D  349 ARG cc_start: 0.8653 (mtt180) cc_final: 0.7272 (mmp-170)
REVERT: D  379 ARG cc_start: 0.5605 (OUTLIER) cc_final: 0.5187 (mtt-85)
REVERT: E  325 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8699 (tt)
REVERT: E  349 ARG cc_start: 0.8618 (mtt180) cc_final: 0.7156 (mmp-170)
REVERT: E  379 ARG cc_start: 0.5382 (OUTLIER) cc_final: 0.4281 (mtt-85)
  outliers start: 5
  outliers final: 1
  residues processed: 86
  average time/residue: 0.5849
  time to fit residues: 51.3086
Evaluate side-chains
  88 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 18 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 7 optimal weight:    8.9990
   chunk 14 optimal weight:    8.9990
   chunk 5 optimal weight:    9.9990
   chunk 32 optimal weight:    6.9990
   chunk 1 optimal weight:   10.0000
   chunk 31 optimal weight:    7.9990
   chunk 22 optimal weight:    0.4980
   chunk 15 optimal weight:    6.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    4.4988

-------------------------------------------------------------------------------
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 = 0.3884 r_free = 0.3884 target = 0.123667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.106964 restraints weight = 3108.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 1.29
r_work: 0.3501 rms_B_bonded: 1.45 restraints_weight: 0.5000
r_work: 0.3418 rms_B_bonded: 2.43 restraints_weight: 0.2500
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9051
moved from start:          0.3564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   2915  Z= 0.246
  Angle     :  0.748   9.510   3900  Z= 0.375
  Chirality :  0.053   0.143    440
  Planarity :  0.003   0.016    495
  Dihedral  :  5.356  16.134    385
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 19.39 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.001   0.000   ARG D 379 
 TYR   0.009   0.002   TYR E 310 
 PHE   0.009   0.002   PHE C 378 
 HIS   0.003   0.001   HIS D 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00599 ( 2915)
  covalent geometry    : angle       0.74765 ( 3900)
  hydrogen bonds       : bond        0.02841 (   64)
  hydrogen bonds       : angle       5.05908 (  192)

********************** 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
  91 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.083 
Fit side-chains
REVERT: C  317 LYS cc_start: 0.8811 (mtmt) cc_final: 0.8489 (mttm)
REVERT: D  325 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8872 (tt)
REVERT: D  349 ARG cc_start: 0.8660 (mtt180) cc_final: 0.7260 (mmp-170)
REVERT: D  379 ARG cc_start: 0.5534 (OUTLIER) cc_final: 0.5180 (mtt-85)
REVERT: E  325 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8893 (tt)
REVERT: E  349 ARG cc_start: 0.8609 (mtt180) cc_final: 0.7320 (mmp-170)
REVERT: E  379 ARG cc_start: 0.5505 (OUTLIER) cc_final: 0.5255 (mtt-85)
  outliers start: 7
  outliers final: 2
  residues processed: 88
  average time/residue: 0.6022
  time to fit residues: 54.0464
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  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 ARG
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 17 optimal weight:    0.6980
   chunk 15 optimal weight:    8.9990
   chunk 26 optimal weight:    4.9990
   chunk 13 optimal weight:    6.9990
   chunk 14 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    0.8980
   overall best weight:    3.3186

-------------------------------------------------------------------------------
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 = 0.3900 r_free = 0.3900 target = 0.124980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.108387 restraints weight = 3083.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 1.30
r_work: 0.3521 rms_B_bonded: 1.46 restraints_weight: 0.5000
r_work: 0.3439 rms_B_bonded: 2.45 restraints_weight: 0.2500
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9041
moved from start:          0.3537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   2915  Z= 0.189
  Angle     :  0.703   9.180   3900  Z= 0.355
  Chirality :  0.051   0.139    440
  Planarity :  0.002   0.014    495
  Dihedral  :  5.262  15.664    385
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 1.71
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.77 (0.34), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.34 (0.26), residues: 365

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 2915)
  covalent geometry    : angle       0.70321 ( 3900)
  hydrogen bonds       : bond        0.02521 (   64)
  hydrogen bonds       : angle       4.91630 (  192)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1972.56 seconds
wall clock time: 34 minutes 17.50 seconds (2057.50 seconds total)