Starting phenix.real_space_refine
on Tue Feb 11 22:27:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tew_25853/02_2025/7tew_25853.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tew_25853/02_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_25853/02_2025/7tew_25853.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tew_25853/02_2025/7tew_25853.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tew_25853/02_2025/7tew_25853.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tew_25853/02_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-5592/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: 5.31, per 1000 atoms: 0.81
  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: 1.43
  Conformation dependent library (CDL) restraints added in 954.4 milliseconds
  

  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: 0.64
  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: 1.71

  Time building geometry restraints manager: 1.71 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:             4.010
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.170
  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:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.310
-------------------------------------------------------------------------------
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  : 0.730 
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: 0.2534
  time to fit residues: 42.3126
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  : 0.788 
-------------------------------------------------------------------------------
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 = 41)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.053431 restraints weight = 26158.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.055532 restraints weight = 12795.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.056893 restraints weight = 8043.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
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  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  417 LYS cc_start: 0.9460 (mmmt) cc_final: 0.9062 (mmmt)
REVERT: B  424 LYS cc_start: 0.8702 (tptt) cc_final: 0.8349 (tppt)
REVERT: B  448 ASN cc_start: 0.9218 (t0) cc_final: 0.8836 (t0)
REVERT: B  458 LYS cc_start: 0.9305 (mtmt) cc_final: 0.9071 (mtmm)
REVERT: B  467 ASP cc_start: 0.8280 (t0) cc_final: 0.7928 (t0)
REVERT: E  108 LEU cc_start: 0.8538 (tp) cc_final: 0.8164 (tp)
REVERT: E  232 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8805 (mp0)
REVERT: E  302 TRP cc_start: 0.8469 (m-10) cc_final: 0.7668 (m100)
REVERT: E  323 MET cc_start: 0.9516 (mmp) cc_final: 0.9312 (mmm)
REVERT: E  366 MET cc_start: 0.8925 (mtp) cc_final: 0.8583 (mtm)
REVERT: E  498 CYS cc_start: 0.8428 (t) cc_final: 0.8062 (t)
  outliers start: 13
  outliers final: 6
  residues processed: 84
  average time/residue: 0.2036
  time to fit residues: 22.8200
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  : 0.768 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0670
   chunk 46 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 73 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 71 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.3322

-------------------------------------------------------------------------------
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 = 0.3218 r_free = 0.3218 target = 0.063112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.049702 restraints weight = 26659.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.051661 restraints weight = 13271.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.052961 restraints weight = 8540.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.2747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6737  Z= 0.262
  Angle     :  0.552   5.927   9153  Z= 0.287
  Chirality :  0.041   0.147    976
  Planarity :  0.004   0.046   1178
  Dihedral  :  5.185  53.434   1013
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  8.86 %
    Favored  : 89.14 %
  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 (0.29), residues: 793
  helix:  1.68 (0.26), residues: 412
  sheet:  0.51 (0.68), residues: 51
  loop :  0.21 (0.33), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP E 165 
 HIS   0.005   0.001   HIS E  34 
 PHE   0.016   0.002   PHE E 369 
 TYR   0.019   0.001   TYR E 613 
 ARG   0.003   0.001   ARG B 452 

*********************** 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
  72 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  386 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7933 (ptmm)
REVERT: B  409 GLN cc_start: 0.9300 (mt0) cc_final: 0.9024 (mt0)
REVERT: B  448 ASN cc_start: 0.9260 (t0) cc_final: 0.8864 (t0)
REVERT: B  467 ASP cc_start: 0.8235 (t0) cc_final: 0.7952 (t0)
REVERT: E   22 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8625 (mm-30)
REVERT: E   62 MET cc_start: 0.9480 (mtp) cc_final: 0.9141 (mtm)
REVERT: E  108 LEU cc_start: 0.8548 (tp) cc_final: 0.8134 (tp)
REVERT: E  232 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8856 (mp0)
REVERT: E  366 MET cc_start: 0.8991 (mtp) cc_final: 0.8645 (mtm)
REVERT: E  435 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8795 (mp0)
REVERT: E  498 CYS cc_start: 0.8815 (t) cc_final: 0.8461 (t)
  outliers start: 14
  outliers final: 8
  residues processed: 70
  average time/residue: 0.1774
  time to fit residues: 17.0942
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
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  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  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:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0870
   chunk 29 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   overall best weight:    1.1360

-------------------------------------------------------------------------------
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 = 0.3211 r_free = 0.3211 target = 0.062804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.049120 restraints weight = 27307.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.051051 restraints weight = 13706.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.052362 restraints weight = 8896.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.3072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6737  Z= 0.233
  Angle     :  0.535  10.100   9153  Z= 0.273
  Chirality :  0.040   0.140    976
  Planarity :  0.004   0.044   1178
  Dihedral  :  5.067  54.623   1013
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 10.29 %
    Favored  : 87.71 %
  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:  1.43 (0.30), residues: 793
  helix:  1.66 (0.26), residues: 415
  sheet:  0.47 (0.69), residues: 51
  loop :  0.22 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.013   0.001   TYR B 453 
 ARG   0.003   0.000   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  : 0.727 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  409 GLN cc_start: 0.9329 (mt0) cc_final: 0.9111 (mt0)
REVERT: B  448 ASN cc_start: 0.9276 (t0) cc_final: 0.8864 (t0)
REVERT: B  467 ASP cc_start: 0.8221 (t0) cc_final: 0.7878 (t0)
REVERT: E   22 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8638 (mm-30)
REVERT: E   62 MET cc_start: 0.9474 (OUTLIER) cc_final: 0.9212 (mtp)
REVERT: E  208 GLU cc_start: 0.8784 (tt0) cc_final: 0.8444 (tm-30)
REVERT: E  277 ASN cc_start: 0.9152 (OUTLIER) cc_final: 0.8621 (t0)
REVERT: E  366 MET cc_start: 0.9008 (mtp) cc_final: 0.8716 (mtp)
REVERT: E  435 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8694 (mp0)
REVERT: E  498 CYS cc_start: 0.9092 (t) cc_final: 0.8693 (t)
  outliers start: 14
  outliers final: 9
  residues processed: 63
  average time/residue: 0.1836
  time to fit residues: 16.0568
Evaluate side-chains
  60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
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  435 GLU
Chi-restraints excluded: chain E residue  468 ILE
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 30 optimal weight:    8.9990
   chunk 48 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 5 optimal weight:    0.1980
   chunk 6 optimal weight:    0.0870
   chunk 24 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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 = 0.3240 r_free = 0.3240 target = 0.063675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.050275 restraints weight = 26927.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.052291 restraints weight = 13071.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.053604 restraints weight = 8258.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.3198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6737  Z= 0.161
  Angle     :  0.500   7.114   9153  Z= 0.256
  Chirality :  0.039   0.134    976
  Planarity :  0.004   0.042   1178
  Dihedral  :  4.790  55.455   1013
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 11.29 %
    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:  1.54 (0.30), residues: 793
  helix:  1.74 (0.26), residues: 415
  sheet:  0.69 (0.77), residues: 41
  loop :  0.26 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.012   0.001   PHE E 369 
 TYR   0.010   0.001   TYR B 453 
 ARG   0.002   0.000   ARG B 408 

*********************** 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
  65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 52
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  386 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7887 (ptmm)
REVERT: B  409 GLN cc_start: 0.9345 (mt0) cc_final: 0.9133 (mt0)
REVERT: B  424 LYS cc_start: 0.8815 (tptt) cc_final: 0.8323 (tppt)
REVERT: B  448 ASN cc_start: 0.9250 (t0) cc_final: 0.8854 (t0)
REVERT: B  467 ASP cc_start: 0.8111 (t0) cc_final: 0.7762 (t0)
REVERT: E   62 MET cc_start: 0.9473 (OUTLIER) cc_final: 0.9183 (mtp)
REVERT: E  108 LEU cc_start: 0.8510 (tp) cc_final: 0.8138 (tp)
REVERT: E  208 GLU cc_start: 0.8814 (tt0) cc_final: 0.8480 (tm-30)
REVERT: E  277 ASN cc_start: 0.9175 (OUTLIER) cc_final: 0.8654 (t0)
REVERT: E  366 MET cc_start: 0.8992 (mtp) cc_final: 0.8722 (mtp)
REVERT: E  435 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8640 (mp0)
REVERT: E  498 CYS cc_start: 0.9035 (t) cc_final: 0.8691 (t)
  outliers start: 13
  outliers final: 5
  residues processed: 62
  average time/residue: 0.2017
  time to fit residues: 16.9897
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  386 LYS
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  435 GLU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 20 optimal weight:    7.9990
   chunk 44 optimal weight:    5.9990
   chunk 30 optimal weight:    8.9990
   chunk 45 optimal weight:    1.9990
   chunk 7 optimal weight:    0.1980
   chunk 31 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.3201 r_free = 0.3201 target = 0.062231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.048470 restraints weight = 26912.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.050391 restraints weight = 13700.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.051676 restraints weight = 8901.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.3405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6737  Z= 0.240
  Angle     :  0.521   5.651   9153  Z= 0.271
  Chirality :  0.040   0.135    976
  Planarity :  0.004   0.041   1178
  Dihedral  :  4.909  55.411   1013
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 11.57 %
    Favored  : 85.86 %
  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:  1.59 (0.30), residues: 793
  helix:  1.73 (0.26), residues: 416
  sheet:  0.41 (0.69), residues: 51
  loop :  0.41 (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   0.020   0.001   TYR E 613 
 ARG   0.002   0.000   ARG E 169 

*********************** 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
  68 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 50
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  409 GLN cc_start: 0.9338 (mt0) cc_final: 0.9067 (mt0)
REVERT: B  424 LYS cc_start: 0.8837 (tptt) cc_final: 0.8430 (tppt)
REVERT: B  448 ASN cc_start: 0.9272 (t0) cc_final: 0.8870 (t0)
REVERT: B  467 ASP cc_start: 0.8164 (t0) cc_final: 0.7775 (t0)
REVERT: E   62 MET cc_start: 0.9487 (OUTLIER) cc_final: 0.9220 (mtp)
REVERT: E  108 LEU cc_start: 0.8500 (tp) cc_final: 0.8118 (tp)
REVERT: E  208 GLU cc_start: 0.8823 (tt0) cc_final: 0.8523 (tm-30)
REVERT: E  277 ASN cc_start: 0.9225 (OUTLIER) cc_final: 0.8739 (t0)
REVERT: E  366 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8671 (mtp)
REVERT: E  435 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8642 (mp0)
REVERT: E  498 CYS cc_start: 0.9194 (t) cc_final: 0.8691 (t)
  outliers start: 18
  outliers final: 11
  residues processed: 64
  average time/residue: 0.1929
  time to fit residues: 16.8859
Evaluate side-chains
  62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
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   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  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:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   chunk 51 optimal weight:    0.2980
   chunk 29 optimal weight:    3.9990
   chunk 76 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3213 r_free = 0.3213 target = 0.062765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.049330 restraints weight = 26514.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.051254 restraints weight = 13331.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.052524 restraints weight = 8607.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.3444

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= 0.174
  Angle     :  0.504   6.489   9153  Z= 0.257
  Chirality :  0.039   0.132    976
  Planarity :  0.003   0.040   1178
  Dihedral  :  4.741  55.865   1013
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 12.57 %
    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:  1.60 (0.30), residues: 793
  helix:  1.73 (0.26), residues: 417
  sheet:  0.68 (0.79), residues: 41
  loop :  0.38 (0.34), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 
 PHE   0.012   0.001   PHE E 369 
 TYR   0.010   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
  66 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
REVERT: B  409 GLN cc_start: 0.9334 (mt0) cc_final: 0.9072 (mt0)
REVERT: B  424 LYS cc_start: 0.8855 (tptt) cc_final: 0.8414 (tppt)
REVERT: B  444 LYS cc_start: 0.9122 (ptpp) cc_final: 0.8895 (ptpp)
REVERT: B  467 ASP cc_start: 0.8101 (t0) cc_final: 0.7771 (t0)
REVERT: E   62 MET cc_start: 0.9477 (OUTLIER) cc_final: 0.9251 (mtp)
REVERT: E  208 GLU cc_start: 0.8837 (tt0) cc_final: 0.8544 (tm-30)
REVERT: E  277 ASN cc_start: 0.9202 (OUTLIER) cc_final: 0.8782 (t0)
REVERT: E  366 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8731 (mtp)
REVERT: E  435 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8686 (mp0)
REVERT: E  474 MET cc_start: 0.8274 (mmp) cc_final: 0.8068 (mmm)
REVERT: E  498 CYS cc_start: 0.9158 (t) cc_final: 0.8707 (t)
  outliers start: 14
  outliers final: 6
  residues processed: 63
  average time/residue: 0.2141
  time to fit residues: 18.1377
Evaluate side-chains
  58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  430 THR
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:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 68 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    1.4986

-------------------------------------------------------------------------------
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 = 0.3168 r_free = 0.3168 target = 0.060904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.047317 restraints weight = 27184.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.049229 restraints weight = 13550.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.050485 restraints weight = 8717.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.3649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6737  Z= 0.287
  Angle     :  0.558   8.467   9153  Z= 0.286
  Chirality :  0.041   0.138    976
  Planarity :  0.004   0.041   1178
  Dihedral  :  5.030  55.474   1013
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 13.29 %
    Favored  : 84.43 %
  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:  1.58 (0.30), residues: 793
  helix:  1.71 (0.26), residues: 415
  sheet:  0.31 (0.70), residues: 51
  loop :  0.45 (0.35), residues: 327

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   0.015   0.001   PHE E 369 
 TYR   0.015   0.001   TYR B 453 
 ARG   0.002   0.000   ARG B 403 

*********************** 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
  65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 49
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  409 GLN cc_start: 0.9343 (mt0) cc_final: 0.9062 (mt0)
REVERT: B  424 LYS cc_start: 0.8881 (tptt) cc_final: 0.8499 (tppt)
REVERT: B  467 ASP cc_start: 0.8120 (t0) cc_final: 0.7813 (t0)
REVERT: E   62 MET cc_start: 0.9461 (OUTLIER) cc_final: 0.9172 (mtp)
REVERT: E  208 GLU cc_start: 0.8853 (tt0) cc_final: 0.8575 (tm-30)
REVERT: E  249 MET cc_start: 0.8579 (ttm) cc_final: 0.7986 (mtp)
REVERT: E  277 ASN cc_start: 0.9248 (OUTLIER) cc_final: 0.8855 (t0)
REVERT: E  288 LYS cc_start: 0.9129 (tppt) cc_final: 0.8841 (tppt)
REVERT: E  366 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8678 (mtp)
REVERT: E  435 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8712 (mp0)
REVERT: E  498 CYS cc_start: 0.9240 (t) cc_final: 0.8890 (t)
  outliers start: 16
  outliers final: 9
  residues processed: 62
  average time/residue: 0.2184
  time to fit residues: 18.3155
Evaluate side-chains
  61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
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  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:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 43 optimal weight:    9.9990
   chunk 51 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 30 optimal weight:    7.9990
   chunk 22 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3193 r_free = 0.3193 target = 0.061875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.048158 restraints weight = 27251.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.050053 restraints weight = 13880.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.051320 restraints weight = 9074.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.3665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6737  Z= 0.203
  Angle     :  0.522   7.863   9153  Z= 0.265
  Chirality :  0.040   0.132    976
  Planarity :  0.003   0.042   1178
  Dihedral  :  4.833  55.771   1013
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 14.00 %
    Favored  : 84.14 %
  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:  1.61 (0.30), residues: 793
  helix:  1.72 (0.26), residues: 416
  sheet:  0.29 (0.70), residues: 51
  loop :  0.48 (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   0.012   0.001   PHE E 369 
 TYR   0.010   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
  62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  409 GLN cc_start: 0.9348 (mt0) cc_final: 0.9100 (mt0)
REVERT: B  424 LYS cc_start: 0.8886 (tptt) cc_final: 0.8459 (tppt)
REVERT: B  467 ASP cc_start: 0.8089 (t0) cc_final: 0.7808 (t0)
REVERT: E   62 MET cc_start: 0.9489 (OUTLIER) cc_final: 0.9251 (mtp)
REVERT: E  208 GLU cc_start: 0.8852 (tt0) cc_final: 0.8587 (tm-30)
REVERT: E  249 MET cc_start: 0.8575 (ttm) cc_final: 0.7931 (mtp)
REVERT: E  277 ASN cc_start: 0.9200 (OUTLIER) cc_final: 0.8810 (t0)
REVERT: E  288 LYS cc_start: 0.9164 (tppt) cc_final: 0.8912 (tppt)
REVERT: E  366 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8668 (mtp)
REVERT: E  435 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8687 (mp0)
REVERT: E  498 CYS cc_start: 0.9212 (t) cc_final: 0.8711 (t)
  outliers start: 13
  outliers final: 7
  residues processed: 59
  average time/residue: 0.2179
  time to fit residues: 17.2965
Evaluate side-chains
  58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  430 THR
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 33 optimal weight:    6.9990
   chunk 10 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3195 r_free = 0.3195 target = 0.061949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.048247 restraints weight = 27376.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.050166 restraints weight = 13849.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.051425 restraints weight = 9020.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.3692

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= 0.195
  Angle     :  0.522   7.425   9153  Z= 0.264
  Chirality :  0.040   0.133    976
  Planarity :  0.003   0.042   1178
  Dihedral  :  4.768  55.821   1013
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 14.14 %
    Favored  : 84.29 %
  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:  1.65 (0.30), residues: 793
  helix:  1.76 (0.26), residues: 416
  sheet:  0.27 (0.71), residues: 51
  loop :  0.51 (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   0.012   0.001   PHE E 369 
 TYR   0.010   0.001   TYR B 453 
 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
  61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  409 GLN cc_start: 0.9346 (mt0) cc_final: 0.9117 (mt0)
REVERT: B  424 LYS cc_start: 0.8878 (tptt) cc_final: 0.8464 (tppt)
REVERT: B  467 ASP cc_start: 0.8069 (t0) cc_final: 0.7808 (t0)
REVERT: E   62 MET cc_start: 0.9490 (OUTLIER) cc_final: 0.9266 (mtp)
REVERT: E  208 GLU cc_start: 0.8839 (tt0) cc_final: 0.8577 (tm-30)
REVERT: E  249 MET cc_start: 0.8580 (ttm) cc_final: 0.7894 (mtp)
REVERT: E  277 ASN cc_start: 0.9224 (OUTLIER) cc_final: 0.8983 (t0)
REVERT: E  288 LYS cc_start: 0.9143 (tppt) cc_final: 0.8874 (tppt)
REVERT: E  435 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8672 (mp0)
REVERT: E  498 CYS cc_start: 0.9172 (t) cc_final: 0.8735 (t)
  outliers start: 11
  outliers final: 8
  residues processed: 59
  average time/residue: 0.2238
  time to fit residues: 17.6117
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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:    0.1980
   chunk 55 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 60 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3208 r_free = 0.3208 target = 0.062489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.048724 restraints weight = 27516.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.050672 restraints weight = 13916.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.051940 restraints weight = 9056.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.3712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6737  Z= 0.178
  Angle     :  0.521   7.301   9153  Z= 0.262
  Chirality :  0.039   0.130    976
  Planarity :  0.003   0.042   1178
  Dihedral  :  4.674  55.984   1013
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 14.14 %
    Favored  : 84.29 %
  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:  1.67 (0.30), residues: 793
  helix:  1.77 (0.26), residues: 416
  sheet:  0.25 (0.72), residues: 51
  loop :  0.53 (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   0.012   0.001   PHE E 369 
 TYR   0.009   0.001   TYR B 453 
 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: 2222.69 seconds
wall clock time: 40 minutes 41.35 seconds (2441.35 seconds total)