Starting phenix.real_space_refine
on Tue Mar 11 21:56:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tew_25853/03_2025/7tew_25853.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tew_25853/03_2025/7tew_25853.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tew_25853/03_2025/7tew_25853.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tew_25853/03_2025/7tew_25853.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tew_25853/03_2025/7tew_25853.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tew_25853/03_2025/7tew_25853.cif"
  }
  resolution = 3.52
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.013
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      37      5.16       5
     C    4188      2.51       5
     N    1082      2.21       5
     O    1248      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6555
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1595
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 11, 'TRANS': 189}
    Chain: "E"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 5.01, per 1000 atoms: 0.76
  Number of scatterers: 6555
  At special positions: 0
  Unit cell: (80, 86, 122, 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      37     16.00
     O    1248      8.00
     N    1082      7.00
     C    4188      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 133 " - pdb=" SG  CYS E 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 530 " - pdb=" SG  CYS E 542 " distance=2.03

  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
  Links applied
    NAG-ASN
      " NAG B1301 " - " ASN B 343 "
      " NAG E 701 " - " ASN E  53 "
      " NAG E 702 " - " ASN E  90 "
      " NAG E 703 " - " ASN E 103 "
      " NAG E 704 " - " ASN E 322 "
      " NAG E 705 " - " ASN E 432 "
      " NAG E 706 " - " ASN E 546 "
  Time building additional restraints: 1.46
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1500

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 7 sheets defined
      57.0% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 365 through 370
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.752A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 53
      removed outlier: 4.114A  pdb=" N   ASP E  38 " --> pdb=" O   HIS E  34 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   LEU E  39 " --> pdb=" O   GLU E  35 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 81
    Processing helix  chain 'E' and resid 82 through 83
      No H-bonds generated for 'chain 'E' and resid 82 through 83'
    Processing helix  chain 'E' and resid 84 through 88
      removed outlier: 3.753A  pdb=" N   GLU E  87 " --> pdb=" O   PRO E  84 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 101
    Processing helix  chain 'E' and resid 103 through 108
      removed outlier: 4.041A  pdb=" N   VAL E 107 " --> pdb=" O   GLY E 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 109 through 129
    Processing helix  chain 'E' and resid 146 through 155
      removed outlier: 4.045A  pdb=" N   ILE E 151 " --> pdb=" O   GLY E 147 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 157 through 194
      Proline residue:  E 178  - end of helix
      removed outlier: 3.697A  pdb=" N   VAL E 185 " --> pdb=" O   GLU E 181 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 198 through 205
    Processing helix  chain 'E' and resid 206 through 208
      No H-bonds generated for 'chain 'E' and resid 206 through 208'
    Processing helix  chain 'E' and resid 220 through 252
      removed outlier: 3.928A  pdb=" N   GLU E 224 " --> pdb=" O   GLY E 220 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   GLU E 232 " --> pdb=" O   HIS E 228 " (cutoff:3.500A)
      Proline residue:  E 235  - end of helix
    Processing helix  chain 'E' and resid 265 through 267
      No H-bonds generated for 'chain 'E' and resid 265 through 267'
    Processing helix  chain 'E' and resid 275 through 279
      removed outlier: 3.811A  pdb=" N   TYR E 279 " --> pdb=" O   THR E 276 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 293 through 300
    Processing helix  chain 'E' and resid 303 through 319
    Processing helix  chain 'E' and resid 324 through 331
      removed outlier: 3.521A  pdb=" N   TRP E 328 " --> pdb=" O   THR E 324 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 385
      removed outlier: 3.689A  pdb=" N   TYR E 385 " --> pdb=" O   TYR E 381 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 386 through 388
      No H-bonds generated for 'chain 'E' and resid 386 through 388'
    Processing helix  chain 'E' and resid 389 through 393
    Processing helix  chain 'E' and resid 397 through 413
      removed outlier: 4.289A  pdb=" N   HIS E 401 " --> pdb=" O   ASN E 397 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   GLU E 402 " --> pdb=" O   GLU E 398 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   GLY E 405 " --> pdb=" O   HIS E 401 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   MET E 408 " --> pdb=" O   VAL E 404 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 414 through 421
    Processing helix  chain 'E' and resid 431 through 447
      removed outlier: 3.511A  pdb=" N   GLU E 435 " --> pdb=" O   ASP E 431 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 448 through 465
      removed outlier: 4.328A  pdb=" N   PHE E 452 " --> pdb=" O   GLY E 448 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 469 through 471
      No H-bonds generated for 'chain 'E' and resid 469 through 471'
    Processing helix  chain 'E' and resid 472 through 484
    Processing helix  chain 'E' and resid 499 through 502
      removed outlier: 3.648A  pdb=" N   SER E 502 " --> pdb=" O   ASP E 499 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 499 through 502'
    Processing helix  chain 'E' and resid 503 through 508
    Processing helix  chain 'E' and resid 513 through 533
      removed outlier: 3.614A  pdb=" N   PHE E 523 " --> pdb=" O   THR E 519 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 538 through 542
    Processing helix  chain 'E' and resid 547 through 559
      removed outlier: 3.896A  pdb=" N   MET E 557 " --> pdb=" O   LYS E 553 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 565 through 574
    Processing helix  chain 'E' and resid 581 through 588
    Processing helix  chain 'E' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358
      removed outlier: 4.002A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392
    Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'E' and resid 131 through 132
      removed outlier: 3.774A  pdb=" N   LEU E 142 " --> pdb=" O   VAL E 132 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 262 through 263
      removed outlier: 6.158A  pdb=" N   LEU E 262 " --> pdb=" O   VAL E 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 347 through 352
      removed outlier: 6.347A  pdb=" N   ASP E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)

    322 hydrogen bonds defined for protein.
    915 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.65

  Time building geometry restraints manager: 1.77 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2087
        1.35 -     1.47: 1795
        1.47 -     1.60: 2797
        1.60 -     1.73: 0
        1.73 -     1.85: 58
  Bond restraints: 6737
  Sorted by residual:
  bond pdb=" C1  NAG E 706 "
       pdb=" O5  NAG E 706 "
    ideal  model  delta    sigma   weight residual
    1.406  1.462 -0.056 2.00e-02 2.50e+03 7.80e+00
  bond pdb=" C1  NAG E 702 "
       pdb=" O5  NAG E 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.460 -0.054 2.00e-02 2.50e+03 7.22e+00
  bond pdb=" C1  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.455 -0.049 2.00e-02 2.50e+03 5.99e+00
  bond pdb=" C1  NAG E 704 "
       pdb=" O5  NAG E 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.447 -0.041 2.00e-02 2.50e+03 4.19e+00
  bond pdb=" C1  NAG E 703 "
       pdb=" O5  NAG E 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.447 -0.041 2.00e-02 2.50e+03 4.15e+00
  ... (remaining 6732 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 8757
        1.91 -     3.82: 350
        3.82 -     5.73: 34
        5.73 -     7.63: 8
        7.63 -     9.54: 4
  Bond angle restraints: 9153
  Sorted by residual:
  angle pdb=" C   SER B 359 "
        pdb=" N   ASN B 360 "
        pdb=" CA  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     122.36  128.24   -5.88 1.42e+00 4.96e-01 1.71e+01
  angle pdb=" CA  CYS E 141 "
        pdb=" CB  CYS E 141 "
        pdb=" SG  CYS E 141 "
      ideal   model   delta    sigma   weight residual
     114.40  122.95   -8.55 2.30e+00 1.89e-01 1.38e+01
  angle pdb=" C   HIS E  34 "
        pdb=" N   GLU E  35 "
        pdb=" CA  GLU E  35 "
      ideal   model   delta    sigma   weight residual
     122.38  115.72    6.66 1.81e+00 3.05e-01 1.35e+01
  angle pdb=" CA  ASN E 437 "
        pdb=" CB  ASN E 437 "
        pdb=" CG  ASN E 437 "
      ideal   model   delta    sigma   weight residual
     112.60  116.25   -3.65 1.00e+00 1.00e+00 1.33e+01
  angle pdb=" CA  LYS E  31 "
        pdb=" CB  LYS E  31 "
        pdb=" CG  LYS E  31 "
      ideal   model   delta    sigma   weight residual
     114.10  120.85   -6.75 2.00e+00 2.50e-01 1.14e+01
  ... (remaining 9148 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.87: 3680
       16.87 -    33.74: 316
       33.74 -    50.61: 51
       50.61 -    67.47: 12
       67.47 -    84.34: 12
  Dihedral angle restraints: 4071
    sinusoidal: 1733
      harmonic: 2338
  Sorted by residual:
  dihedral pdb=" CB  CYS E 133 "
           pdb=" SG  CYS E 133 "
           pdb=" SG  CYS E 141 "
           pdb=" CB  CYS E 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -47.25  -38.75     1      1.00e+01 1.00e-02 2.11e+01
  dihedral pdb=" SG  CYS B 391 "
           pdb=" CB  CYS B 525 "
           pdb=" SG  CYS B 525 "
           pdb=" CA  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   14.06   64.94     1      2.00e+01 2.50e-03 1.38e+01
  dihedral pdb=" C   ASN B 360 "
           pdb=" N   ASN B 360 "
           pdb=" CA  ASN B 360 "
           pdb=" CB  ASN B 360 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.88    8.28     0      2.50e+00 1.60e-01 1.10e+01
  ... (remaining 4068 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 729
       0.056 -    0.111: 186
       0.111 -    0.166: 51
       0.166 -    0.222: 8
       0.222 -    0.277: 2
  Chirality restraints: 976
  Sorted by residual:
  chirality pdb=" CB  VAL E 581 "
            pdb=" CA  VAL E 581 "
            pdb=" CG1 VAL E 581 "
            pdb=" CG2 VAL E 581 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" CA  ASN B 360 "
            pdb=" N   ASN B 360 "
            pdb=" C   ASN B 360 "
            pdb=" CB  ASN B 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" C1  NAG E 703 "
            pdb=" ND2 ASN E 103 "
            pdb=" C2  NAG E 703 "
            pdb=" O5  NAG E 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.19   -0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 973 not shown)

  Planarity restraints: 1185
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU E 589 "   -0.052 5.00e-02 4.00e+02   7.79e-02 9.70e+00
        pdb=" N   PRO E 590 "    0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO E 590 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO E 590 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E 499 "   -0.048 5.00e-02 4.00e+02   7.10e-02 8.06e+00
        pdb=" N   PRO E 500 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO E 500 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO E 500 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 495 "   -0.021 2.00e-02 2.50e+03   1.86e-02 6.95e+00
        pdb=" CG  TYR B 495 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 495 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 495 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 495 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 495 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 495 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR B 495 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1182 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.86: 2224
        2.86 -     3.37: 5996
        3.37 -     3.88: 11266
        3.88 -     4.39: 12492
        4.39 -     4.90: 21655
  Nonbonded interactions: 53633
  Sorted by model distance:
  nonbonded pdb=" O   ASN E 117 "
            pdb=" ND2 ASN E 121 "
     model   vdw
     2.344 3.120
  nonbonded pdb=" OH  TYR E 183 "
            pdb=" OD1 ASP E 509 "
     model   vdw
     2.346 3.040
  nonbonded pdb=" OD1 ASN B 487 "
            pdb=" OH  TYR E  83 "
     model   vdw
     2.365 3.040
  nonbonded pdb=" O   SER E  47 "
            pdb=" ND2 ASN E  51 "
     model   vdw
     2.374 3.120
  nonbonded pdb=" O   MET E 152 "
            pdb=" NH1 ARG E 161 "
     model   vdw
     2.387 3.120
  ... (remaining 53628 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 group one per residue
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:             4.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     18.980
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
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      :  0.005   0.064   6737  Z= 0.314
  Angle     :  0.852   9.543   9153  Z= 0.488
  Chirality :  0.057   0.277    976
  Planarity :  0.008   0.078   1178
  Dihedral  : 13.336  84.341   2553
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.29 %
    Favored  : 96.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.00 (0.25), residues: 793
  helix:  0.53 (0.22), residues: 392
  sheet:  0.98 (0.72), residues: 43
  loop : -0.64 (0.28), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E  69 
 HIS   0.011   0.002   HIS E  34 
 PHE   0.027   0.003   PHE E 369 
 TYR   0.045   0.003   TYR B 495 
 ARG   0.009   0.001   ARG E 460 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 134
  time to evaluate  : 0.744 
Fit side-chains
   revert: symmetry clash
REVERT: B  356 LYS cc_start: 0.8821 (ttmm) cc_final: 0.8482 (ttpt)
REVERT: B  424 LYS cc_start: 0.8692 (tptt) cc_final: 0.8170 (tppt)
REVERT: B  448 ASN cc_start: 0.9203 (t0) cc_final: 0.8698 (t0)
REVERT: B  458 LYS cc_start: 0.9307 (mtmt) cc_final: 0.9072 (mtmm)
REVERT: B  467 ASP cc_start: 0.8432 (t0) cc_final: 0.8085 (t0)
REVERT: B  473 TYR cc_start: 0.9316 (t80) cc_final: 0.9062 (t80)
REVERT: B  474 GLN cc_start: 0.8885 (tt0) cc_final: 0.8616 (tt0)
REVERT: E  108 LEU cc_start: 0.8613 (tp) cc_final: 0.8360 (tp)
REVERT: E  249 MET cc_start: 0.8484 (ttm) cc_final: 0.8082 (mtp)
REVERT: E  297 MET cc_start: 0.9202 (mtm) cc_final: 0.8996 (mtm)
REVERT: E  302 TRP cc_start: 0.8366 (m-10) cc_final: 0.7320 (m100)
REVERT: E  498 CYS cc_start: 0.8204 (t) cc_final: 0.7637 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 135
  average time/residue: 0.2503
  time to fit residues: 42.0808
Evaluate side-chains
  64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    0.0370
   chunk 59 optimal weight:    2.9990
   chunk 33 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0670
   chunk 61 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   overall best weight:    0.6200

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

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 374 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.066767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.053441 restraints weight = 26158.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.055538 restraints weight = 12772.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.056874 restraints weight = 8036.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.2133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6737  Z= 0.176
  Angle     :  0.551   5.787   9153  Z= 0.289
  Chirality :  0.040   0.139    976
  Planarity :  0.005   0.049   1178
  Dihedral  :  5.234  52.822   1013
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  8.29 %
    Favored  : 89.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.07 (0.28), residues: 793
  helix:  1.42 (0.25), residues: 406
  sheet:  1.13 (0.75), residues: 42
  loop : -0.13 (0.30), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.015   0.001   PHE E 428 
 TYR   0.012   0.001   TYR B 453 
 ARG   0.003   0.000   ARG B 452 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.692 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  417 LYS cc_start: 0.9459 (mmmt) cc_final: 0.9062 (mmmt)
REVERT: B  424 LYS cc_start: 0.8704 (tptt) cc_final: 0.8352 (tppt)
REVERT: B  448 ASN cc_start: 0.9217 (t0) cc_final: 0.8835 (t0)
REVERT: B  458 LYS cc_start: 0.9303 (mtmt) cc_final: 0.9069 (mtmm)
REVERT: B  467 ASP cc_start: 0.8276 (t0) cc_final: 0.7928 (t0)
REVERT: E  108 LEU cc_start: 0.8542 (tp) cc_final: 0.8166 (tp)
REVERT: E  232 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8805 (mp0)
REVERT: E  302 TRP cc_start: 0.8473 (m-10) cc_final: 0.7670 (m100)
REVERT: E  323 MET cc_start: 0.9516 (mmp) cc_final: 0.9314 (mmm)
REVERT: E  366 MET cc_start: 0.8926 (mtp) cc_final: 0.8581 (mtm)
REVERT: E  498 CYS cc_start: 0.8441 (t) cc_final: 0.8067 (t)
  outliers start: 13
  outliers final: 6
  residues processed: 84
  average time/residue: 0.1964
  time to fit residues: 21.9628
Evaluate side-chains
  64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain E residue  447 VAL
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 27 optimal weight:    0.2980
   chunk 77 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 73 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.064013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.050621 restraints weight = 26542.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.052595 restraints weight = 13219.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.053902 restraints weight = 8497.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6737  Z= 0.215
  Angle     :  0.528   5.827   9153  Z= 0.274
  Chirality :  0.040   0.142    976
  Planarity :  0.004   0.046   1178
  Dihedral  :  5.029  53.652   1013
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  :  9.00 %
    Favored  : 88.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.42 (0.29), residues: 793
  helix:  1.67 (0.26), residues: 413
  sheet:  0.56 (0.68), residues: 51
  loop :  0.16 (0.32), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.020   0.001   TYR E 613 
 ARG   0.003   0.000   ARG B 403 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  386 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7913 (ptmm)
REVERT: B  409 GLN cc_start: 0.9290 (mt0) cc_final: 0.9023 (mt0)
REVERT: B  448 ASN cc_start: 0.9278 (t0) cc_final: 0.8903 (t0)
REVERT: B  467 ASP cc_start: 0.8244 (t0) cc_final: 0.7949 (t0)
REVERT: E   62 MET cc_start: 0.9480 (OUTLIER) cc_final: 0.9137 (mtm)
REVERT: E  108 LEU cc_start: 0.8543 (tp) cc_final: 0.8124 (tp)
REVERT: E  232 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8846 (mp0)
REVERT: E  267 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9277 (mm)
REVERT: E  302 TRP cc_start: 0.8496 (m100) cc_final: 0.7721 (m100)
REVERT: E  366 MET cc_start: 0.8985 (mtp) cc_final: 0.8651 (mtm)
REVERT: E  435 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8797 (mp0)
REVERT: E  498 CYS cc_start: 0.8800 (t) cc_final: 0.8454 (t)
  outliers start: 15
  outliers final: 8
  residues processed: 72
  average time/residue: 0.1820
  time to fit residues: 18.1037
Evaluate side-chains
  64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  386 LYS
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain E residue   21 ILE
Chi-restraints excluded: chain E residue   62 MET
Chi-restraints excluded: chain E residue  267 LEU
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  579 MET
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 19 optimal weight:    7.9990
   chunk 74 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0050
   chunk 29 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.3998

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

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.062343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.048597 restraints weight = 27427.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.050552 restraints weight = 13786.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.051828 restraints weight = 8936.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6737  Z= 0.271
  Angle     :  0.544   5.827   9153  Z= 0.281
  Chirality :  0.041   0.145    976
  Planarity :  0.004   0.044   1178
  Dihedral  :  5.098  54.502   1013
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 10.14 %
    Favored  : 87.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.48 (0.30), residues: 793
  helix:  1.68 (0.26), residues: 415
  sheet:  0.64 (0.75), residues: 41
  loop :  0.26 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 
 PHE   0.015   0.002   PHE E 369 
 TYR   0.016   0.001   TYR B 453 
 ARG   0.003   0.001   ARG E 169 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  409 GLN cc_start: 0.9255 (mt0) cc_final: 0.8966 (mt0)
REVERT: B  448 ASN cc_start: 0.9285 (t0) cc_final: 0.8879 (t0)
REVERT: B  467 ASP cc_start: 0.8202 (t0) cc_final: 0.7901 (t0)
REVERT: E   62 MET cc_start: 0.9436 (mtp) cc_final: 0.9002 (mtm)
REVERT: E  208 GLU cc_start: 0.8787 (tt0) cc_final: 0.8443 (tm-30)
REVERT: E  277 ASN cc_start: 0.9175 (OUTLIER) cc_final: 0.8619 (t0)
REVERT: E  366 MET cc_start: 0.9007 (mtp) cc_final: 0.8713 (mtp)
REVERT: E  435 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8720 (mp0)
REVERT: E  498 CYS cc_start: 0.9138 (t) cc_final: 0.8794 (t)
  outliers start: 14
  outliers final: 8
  residues processed: 64
  average time/residue: 0.1791
  time to fit residues: 15.9390
Evaluate side-chains
  56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain E residue  277 ASN
Chi-restraints excluded: chain E residue  435 GLU
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 48 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.061653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.048152 restraints weight = 27302.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.050069 restraints weight = 13403.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.051340 restraints weight = 8567.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.3386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6737  Z= 0.264
  Angle     :  0.538   5.881   9153  Z= 0.278
  Chirality :  0.041   0.144    976
  Planarity :  0.004   0.044   1178
  Dihedral  :  5.116  55.052   1013
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 10.57 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.44 (0.30), residues: 793
  helix:  1.61 (0.26), residues: 416
  sheet:  0.33 (0.68), residues: 51
  loop :  0.33 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.015   0.001   TYR B 453 
 ARG   0.003   0.000   ARG B 403 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 48
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
REVERT: B  409 GLN cc_start: 0.9291 (mt0) cc_final: 0.8984 (mt0)
REVERT: B  424 LYS cc_start: 0.8851 (tptt) cc_final: 0.8458 (tppt)
REVERT: B  444 LYS cc_start: 0.9119 (ptpp) cc_final: 0.8913 (ptpp)
REVERT: B  467 ASP cc_start: 0.8169 (t0) cc_final: 0.7809 (t0)
REVERT: E   62 MET cc_start: 0.9460 (OUTLIER) cc_final: 0.9198 (mtp)
REVERT: E  208 GLU cc_start: 0.8814 (tt0) cc_final: 0.8533 (tm-30)
REVERT: E  277 ASN cc_start: 0.9221 (OUTLIER) cc_final: 0.8773 (t0)
REVERT: E  366 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8677 (mtp)
REVERT: E  435 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8654 (mp0)
REVERT: E  498 CYS cc_start: 0.9084 (t) cc_final: 0.8786 (t)
  outliers start: 18
  outliers final: 10
  residues processed: 62
  average time/residue: 0.1988
  time to fit residues: 16.8584
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain E residue   62 MET
Chi-restraints excluded: chain E residue  277 ASN
Chi-restraints excluded: chain E residue  366 MET
Chi-restraints excluded: chain E residue  435 GLU
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  527 GLU
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  579 MET
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 30 optimal weight:    8.9990
   chunk 45 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0970
   chunk 58 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    1.1780

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

Flipped N/Q/H residues before XYZ refinement:
E 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.061574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.047997 restraints weight = 27019.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.049887 restraints weight = 13681.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.051133 restraints weight = 8908.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.3515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6737  Z= 0.240
  Angle     :  0.535   6.003   9153  Z= 0.275
  Chirality :  0.040   0.135    976
  Planarity :  0.004   0.041   1178
  Dihedral  :  5.045  55.392   1013
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 12.14 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.45 (0.30), residues: 793
  helix:  1.62 (0.26), residues: 416
  sheet:  0.27 (0.69), residues: 51
  loop :  0.35 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.012   0.001   TYR B 453 
 ARG   0.002   0.000   ARG B 403 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 46
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  386 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.8054 (pttp)
REVERT: B  409 GLN cc_start: 0.9296 (mt0) cc_final: 0.9041 (mt0)
REVERT: B  424 LYS cc_start: 0.8877 (tptt) cc_final: 0.8473 (tppt)
REVERT: B  467 ASP cc_start: 0.8145 (t0) cc_final: 0.7784 (t0)
REVERT: E   62 MET cc_start: 0.9454 (OUTLIER) cc_final: 0.9179 (mtp)
REVERT: E  208 GLU cc_start: 0.8834 (tt0) cc_final: 0.8560 (tm-30)
REVERT: E  249 MET cc_start: 0.8453 (ttm) cc_final: 0.7954 (mtp)
REVERT: E  277 ASN cc_start: 0.9194 (OUTLIER) cc_final: 0.8679 (t0)
REVERT: E  366 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8671 (mtp)
REVERT: E  435 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8689 (mp0)
REVERT: E  455 MET cc_start: 0.8932 (ttp) cc_final: 0.8386 (ttt)
REVERT: E  474 MET cc_start: 0.8459 (mmp) cc_final: 0.8205 (mmm)
REVERT: E  498 CYS cc_start: 0.9163 (t) cc_final: 0.8880 (t)
  outliers start: 16
  outliers final: 10
  residues processed: 58
  average time/residue: 0.2066
  time to fit residues: 16.3498
Evaluate side-chains
  60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 45
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  386 LYS
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain E residue   21 ILE
Chi-restraints excluded: chain E residue   62 MET
Chi-restraints excluded: chain E residue  277 ASN
Chi-restraints excluded: chain E residue  366 MET
Chi-restraints excluded: chain E residue  435 GLU
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  527 GLU
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  579 MET
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 73 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B 334 ASN
E 277 ASN
** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.060707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.047032 restraints weight = 27177.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.048906 restraints weight = 13869.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.050138 restraints weight = 9059.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.3682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6737  Z= 0.292
  Angle     :  0.553   7.918   9153  Z= 0.285
  Chirality :  0.041   0.138    976
  Planarity :  0.004   0.041   1178
  Dihedral  :  5.158  55.378   1013
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 12.29 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.40 (0.30), residues: 793
  helix:  1.58 (0.26), residues: 415
  sheet: -0.02 (0.67), residues: 51
  loop :  0.38 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.014   0.001   TYR B 453 
 ARG   0.002   0.000   ARG B 408 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 47
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  386 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8077 (pttp)
REVERT: B  409 GLN cc_start: 0.9308 (mt0) cc_final: 0.9025 (mt0)
REVERT: B  424 LYS cc_start: 0.8901 (tptt) cc_final: 0.8526 (tppt)
REVERT: B  467 ASP cc_start: 0.8092 (t0) cc_final: 0.7829 (t0)
REVERT: E   62 MET cc_start: 0.9457 (OUTLIER) cc_final: 0.9181 (mtp)
REVERT: E  208 GLU cc_start: 0.8829 (tt0) cc_final: 0.8574 (tm-30)
REVERT: E  249 MET cc_start: 0.8612 (ttm) cc_final: 0.7995 (mtp)
REVERT: E  277 ASN cc_start: 0.9202 (OUTLIER) cc_final: 0.8763 (t0)
REVERT: E  288 LYS cc_start: 0.9159 (tppt) cc_final: 0.8946 (tppt)
REVERT: E  366 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8697 (mtp)
REVERT: E  435 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8654 (mp0)
REVERT: E  498 CYS cc_start: 0.9112 (t) cc_final: 0.8816 (t)
  outliers start: 16
  outliers final: 10
  residues processed: 60
  average time/residue: 0.1942
  time to fit residues: 15.8928
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  386 LYS
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain E residue   21 ILE
Chi-restraints excluded: chain E residue   62 MET
Chi-restraints excluded: chain E residue  277 ASN
Chi-restraints excluded: chain E residue  366 MET
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  527 GLU
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 33 optimal weight:    7.9990
   chunk 52 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
E 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.061796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.047992 restraints weight = 27212.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.049891 restraints weight = 13903.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.051137 restraints weight = 9087.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.3686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6737  Z= 0.197
  Angle     :  0.512   6.805   9153  Z= 0.262
  Chirality :  0.040   0.135    976
  Planarity :  0.004   0.042   1178
  Dihedral  :  4.923  55.847   1013
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 12.71 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.47 (0.30), residues: 793
  helix:  1.63 (0.26), residues: 416
  sheet:  0.10 (0.69), residues: 51
  loop :  0.41 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.010   0.001   TYR B 453 
 ARG   0.002   0.000   ARG B 408 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 48
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  409 GLN cc_start: 0.9336 (mt0) cc_final: 0.9077 (mt0)
REVERT: B  424 LYS cc_start: 0.8866 (tptt) cc_final: 0.8484 (tppt)
REVERT: B  467 ASP cc_start: 0.8040 (t0) cc_final: 0.7797 (t0)
REVERT: E   62 MET cc_start: 0.9447 (OUTLIER) cc_final: 0.9177 (mtp)
REVERT: E  208 GLU cc_start: 0.8835 (tt0) cc_final: 0.8603 (tm-30)
REVERT: E  277 ASN cc_start: 0.9158 (OUTLIER) cc_final: 0.8850 (t0)
REVERT: E  288 LYS cc_start: 0.9109 (tppt) cc_final: 0.8890 (tppt)
REVERT: E  435 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8694 (mp0)
REVERT: E  455 MET cc_start: 0.8872 (ttp) cc_final: 0.8356 (ttt)
REVERT: E  498 CYS cc_start: 0.9246 (t) cc_final: 0.8790 (t)
  outliers start: 14
  outliers final: 6
  residues processed: 59
  average time/residue: 0.2049
  time to fit residues: 16.2838
Evaluate side-chains
  55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain E residue   62 MET
Chi-restraints excluded: chain E residue  277 ASN
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  527 GLU
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 43 optimal weight:   10.0000
   chunk 51 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 30 optimal weight:    7.9990
   chunk 22 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
E 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.061648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.047933 restraints weight = 27238.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.049848 restraints weight = 13865.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.051105 restraints weight = 9034.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.3727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6737  Z= 0.206
  Angle     :  0.517   6.856   9153  Z= 0.263
  Chirality :  0.040   0.134    976
  Planarity :  0.004   0.042   1178
  Dihedral  :  4.871  55.900   1013
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 13.57 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.51 (0.30), residues: 793
  helix:  1.64 (0.26), residues: 416
  sheet:  0.11 (0.69), residues: 51
  loop :  0.46 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.011   0.001   TYR B 453 
 ARG   0.002   0.000   ARG B 408 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  409 GLN cc_start: 0.9329 (mt0) cc_final: 0.9069 (mt0)
REVERT: B  417 LYS cc_start: 0.9382 (mmmt) cc_final: 0.8867 (mmmt)
REVERT: B  424 LYS cc_start: 0.8869 (tptt) cc_final: 0.8487 (tppt)
REVERT: B  467 ASP cc_start: 0.8080 (t0) cc_final: 0.7815 (t0)
REVERT: E   62 MET cc_start: 0.9443 (OUTLIER) cc_final: 0.9180 (mtp)
REVERT: E  208 GLU cc_start: 0.8837 (tt0) cc_final: 0.8584 (tm-30)
REVERT: E  249 MET cc_start: 0.8482 (ttm) cc_final: 0.7977 (mtp)
REVERT: E  277 ASN cc_start: 0.9125 (OUTLIER) cc_final: 0.8921 (t0)
REVERT: E  288 LYS cc_start: 0.9161 (tppt) cc_final: 0.8949 (tppt)
REVERT: E  435 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8686 (mp0)
REVERT: E  455 MET cc_start: 0.8880 (ttp) cc_final: 0.8389 (ttt)
REVERT: E  498 CYS cc_start: 0.9240 (t) cc_final: 0.8876 (t)
  outliers start: 11
  outliers final: 7
  residues processed: 57
  average time/residue: 0.2075
  time to fit residues: 16.2181
Evaluate side-chains
  55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain E residue   21 ILE
Chi-restraints excluded: chain E residue   62 MET
Chi-restraints excluded: chain E residue  277 ASN
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  527 GLU
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 27 optimal weight:    0.1980
   chunk 33 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 32 optimal weight:   10.0000
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
E 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.062150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.048467 restraints weight = 27163.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.050382 restraints weight = 13700.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.051645 restraints weight = 8897.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.3742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6737  Z= 0.179
  Angle     :  0.510   7.125   9153  Z= 0.258
  Chirality :  0.040   0.132    976
  Planarity :  0.003   0.041   1178
  Dihedral  :  4.768  56.037   1013
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 13.86 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.58 (0.30), residues: 793
  helix:  1.69 (0.26), residues: 416
  sheet:  0.13 (0.70), residues: 51
  loop :  0.50 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.009   0.001   TYR E 385 
 ARG   0.002   0.000   ARG B 408 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  409 GLN cc_start: 0.9338 (mt0) cc_final: 0.9084 (mt0)
REVERT: B  417 LYS cc_start: 0.9369 (mmmt) cc_final: 0.8864 (mmmt)
REVERT: B  424 LYS cc_start: 0.8862 (tptt) cc_final: 0.8482 (tppt)
REVERT: B  467 ASP cc_start: 0.8059 (t0) cc_final: 0.7804 (t0)
REVERT: E   62 MET cc_start: 0.9451 (OUTLIER) cc_final: 0.9085 (mtm)
REVERT: E  208 GLU cc_start: 0.8840 (tt0) cc_final: 0.8575 (tm-30)
REVERT: E  249 MET cc_start: 0.8580 (ttm) cc_final: 0.8160 (mtp)
REVERT: E  277 ASN cc_start: 0.9132 (OUTLIER) cc_final: 0.8888 (t0)
REVERT: E  435 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8680 (mp0)
REVERT: E  455 MET cc_start: 0.8864 (ttp) cc_final: 0.8385 (ttt)
REVERT: E  498 CYS cc_start: 0.9203 (t) cc_final: 0.8708 (t)
  outliers start: 10
  outliers final: 6
  residues processed: 59
  average time/residue: 0.2126
  time to fit residues: 16.9719
Evaluate side-chains
  56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain E residue   21 ILE
Chi-restraints excluded: chain E residue   62 MET
Chi-restraints excluded: chain E residue  277 ASN
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  527 GLU
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 59 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 60 optimal weight:    0.3980
   chunk 51 optimal weight:    0.5980
   chunk 42 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0050
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
E 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.062622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.048967 restraints weight = 27363.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.050881 restraints weight = 13693.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.052171 restraints weight = 8873.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.3773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6737  Z= 0.158
  Angle     :  0.514   8.722   9153  Z= 0.260
  Chirality :  0.039   0.132    976
  Planarity :  0.004   0.040   1178
  Dihedral  :  4.628  56.291   1013
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 13.71 %
    Favored  : 84.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.64 (0.30), residues: 793
  helix:  1.76 (0.26), residues: 416
  sheet:  0.15 (0.70), residues: 51
  loop :  0.51 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.011   0.001   PHE E 369 
 TYR   0.009   0.001   TYR E 385 
 ARG   0.002   0.000   ARG B 408 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2216.20 seconds
wall clock time: 39 minutes 23.59 seconds (2363.59 seconds total)