Starting phenix.real_space_refine
on Tue Sep 24 03:26:07 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tew_25853/09_2024/7tew_25853.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tew_25853/09_2024/7tew_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tew_25853/09_2024/7tew_25853.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tew_25853/09_2024/7tew_25853.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tew_25853/09_2024/7tew_25853.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tew_25853/09_2024/7tew_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-5461/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: 5.05, per 1000 atoms: 0.77
  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: 1.60
  Conformation dependent library (CDL) restraints added in 908.8 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: 0.67
  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: 1.80

  Time building geometry restraints manager: 1.85 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:             3.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.900
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.560
-------------------------------------------------------------------------------
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 fitting.
    rotamer outliers: 1
    poor density    : 134
  time to evaluate  : 0.815 
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: 0.2487
  time to fit residues: 41.9180
Evaluate side-chains
  64 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
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 fitting.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  387 LEU cc_start: 0.9226 (mt) cc_final: 0.8993 (mt)
REVERT: B  417 LYS cc_start: 0.9450 (mmmt) cc_final: 0.9042 (mmmt)
REVERT: B  424 LYS cc_start: 0.8718 (tptt) cc_final: 0.8323 (tppt)
REVERT: B  448 ASN cc_start: 0.9283 (t0) cc_final: 0.8861 (t0)
REVERT: B  458 LYS cc_start: 0.9314 (mtmt) cc_final: 0.9079 (mtmm)
REVERT: B  467 ASP cc_start: 0.8336 (t0) cc_final: 0.7910 (t0)
REVERT: E  108 LEU cc_start: 0.8535 (tp) cc_final: 0.8145 (tp)
REVERT: E  232 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8802 (mp0)
REVERT: E  302 TRP cc_start: 0.8486 (m-10) cc_final: 0.7671 (m100)
REVERT: E  323 MET cc_start: 0.9539 (mmp) cc_final: 0.9303 (mmm)
REVERT: E  366 MET cc_start: 0.8938 (mtp) cc_final: 0.8586 (mtm)
REVERT: E  498 CYS cc_start: 0.8541 (t) cc_final: 0.8127 (t)
  outliers start: 13
  outliers final: 6
  residues processed: 84
  average time/residue: 0.2001
  time to fit residues: 22.3530
Evaluate side-chains
  64 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
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 39 optimal weight:    0.1980
   chunk 22 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    0.8386

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.2601

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= 0.191
  Angle     :  0.518   5.762   9153  Z= 0.267
  Chirality :  0.040   0.138    976
  Planarity :  0.004   0.046   1178
  Dihedral  :  4.936  53.672   1013
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  9.29 %
    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:  1.39 (0.29), residues: 793
  helix:  1.67 (0.26), residues: 413
  sheet:  0.88 (0.76), residues: 41
  loop :  0.08 (0.31), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.020   0.001   TYR E 613 
 ARG   0.003   0.001   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
  74 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  409 GLN cc_start: 0.9338 (mt0) cc_final: 0.8935 (tt0)
REVERT: B  448 ASN cc_start: 0.9280 (t0) cc_final: 0.8898 (t0)
REVERT: B  458 LYS cc_start: 0.9303 (mtmt) cc_final: 0.9065 (mtmm)
REVERT: B  467 ASP cc_start: 0.8311 (t0) cc_final: 0.7956 (t0)
REVERT: E   62 MET cc_start: 0.9431 (OUTLIER) cc_final: 0.8985 (mtm)
REVERT: E  108 LEU cc_start: 0.8539 (tp) cc_final: 0.8119 (tp)
REVERT: E  232 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8831 (mp0)
REVERT: E  267 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9223 (mm)
REVERT: E  302 TRP cc_start: 0.8463 (m-10) cc_final: 0.7727 (m100)
REVERT: E  366 MET cc_start: 0.8986 (mtp) cc_final: 0.8656 (mtm)
REVERT: E  435 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8824 (mp0)
REVERT: E  498 CYS cc_start: 0.8806 (t) cc_final: 0.8410 (t)
  outliers start: 13
  outliers final: 7
  residues processed: 71
  average time/residue: 0.1864
  time to fit residues: 18.2483
Evaluate side-chains
  62 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
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   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 37 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 63 optimal weight:    0.1980
   chunk 43 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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**
E 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6737  Z= 0.167
  Angle     :  0.488   5.649   9153  Z= 0.251
  Chirality :  0.039   0.131    976
  Planarity :  0.004   0.043   1178
  Dihedral  :  4.747  54.832   1013
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  9.71 %
    Favored  : 88.29 %
  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:  1.55 (0.29), residues: 793
  helix:  1.83 (0.26), residues: 407
  sheet:  0.61 (0.75), residues: 43
  loop :  0.19 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.013   0.001   PHE E  32 
 TYR   0.011   0.001   TYR B 453 
 ARG   0.002   0.000   ARG B 403 

*********************** 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
  73 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  386 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7869 (ptmm)
REVERT: B  409 GLN cc_start: 0.9355 (mt0) cc_final: 0.9060 (tt0)
REVERT: B  448 ASN cc_start: 0.9267 (t0) cc_final: 0.8830 (t0)
REVERT: B  458 LYS cc_start: 0.9278 (mtmt) cc_final: 0.9069 (mtmm)
REVERT: B  467 ASP cc_start: 0.8264 (t0) cc_final: 0.7885 (t0)
REVERT: E   62 MET cc_start: 0.9421 (mtp) cc_final: 0.8981 (mtm)
REVERT: E  108 LEU cc_start: 0.8554 (tp) cc_final: 0.8149 (tp)
REVERT: E  208 GLU cc_start: 0.8751 (tt0) cc_final: 0.8492 (tt0)
REVERT: E  232 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8842 (mp0)
REVERT: E  267 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9250 (mm)
REVERT: E  277 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8732 (t0)
REVERT: E  302 TRP cc_start: 0.8548 (m100) cc_final: 0.7905 (m100)
REVERT: E  435 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8731 (mp0)
REVERT: E  455 MET cc_start: 0.8922 (ttp) cc_final: 0.8544 (ttt)
REVERT: E  498 CYS cc_start: 0.9062 (t) cc_final: 0.8604 (t)
  outliers start: 14
  outliers final: 6
  residues processed: 70
  average time/residue: 0.1853
  time to fit residues: 17.8575
Evaluate side-chains
  63 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
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 E residue   21 ILE
Chi-restraints excluded: chain E residue  267 LEU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 56 optimal weight:    5.9990
   chunk 31 optimal weight:    7.9990
   chunk 65 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   overall best weight:    2.5586

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.3554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.047   6737  Z= 0.457
  Angle     :  0.655   7.717   9153  Z= 0.341
  Chirality :  0.044   0.161    976
  Planarity :  0.004   0.044   1178
  Dihedral  :  5.677  54.211   1013
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 10.00 %
    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:  1.33 (0.30), residues: 793
  helix:  1.52 (0.26), residues: 416
  sheet:  0.14 (0.67), residues: 51
  loop :  0.31 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP E 302 
 HIS   0.006   0.001   HIS E  34 
 PHE   0.020   0.002   PHE E 369 
 TYR   0.024   0.002   TYR B 453 
 ARG   0.005   0.001   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
  74 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 52
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
REVERT: B  386 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8082 (ptmm)
REVERT: B  409 GLN cc_start: 0.9363 (mt0) cc_final: 0.9057 (mt0)
REVERT: B  424 LYS cc_start: 0.8891 (tptt) cc_final: 0.8520 (tppt)
REVERT: B  448 ASN cc_start: 0.9328 (t0) cc_final: 0.8898 (t0)
REVERT: B  467 ASP cc_start: 0.8224 (t0) cc_final: 0.7856 (t0)
REVERT: E   62 MET cc_start: 0.9446 (OUTLIER) cc_final: 0.9194 (mtp)
REVERT: E  208 GLU cc_start: 0.8752 (tt0) cc_final: 0.8524 (tm-30)
REVERT: E  249 MET cc_start: 0.8725 (ttm) cc_final: 0.8088 (mtp)
REVERT: E  270 MET cc_start: 0.8397 (tpp) cc_final: 0.8116 (tpp)
REVERT: E  277 ASN cc_start: 0.9314 (OUTLIER) cc_final: 0.8685 (t0)
REVERT: E  323 MET cc_start: 0.9575 (mmp) cc_final: 0.9362 (mmp)
REVERT: E  366 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8625 (mtp)
REVERT: E  435 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8726 (mp0)
REVERT: E  498 CYS cc_start: 0.9243 (t) cc_final: 0.8952 (t)
  outliers start: 22
  outliers final: 11
  residues processed: 70
  average time/residue: 0.2047
  time to fit residues: 19.5637
Evaluate side-chains
  63 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 47
  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  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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 43 optimal weight:    7.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.3521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6737  Z= 0.186
  Angle     :  0.517   6.367   9153  Z= 0.266
  Chirality :  0.040   0.141    976
  Planarity :  0.004   0.041   1178
  Dihedral  :  4.986  55.320   1013
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 12.71 %
    Favored  : 85.71 %
  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:  1.41 (0.30), residues: 793
  helix:  1.59 (0.26), residues: 416
  sheet:  0.20 (0.69), residues: 51
  loop :  0.32 (0.34), residues: 326

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   0.013   0.001   PHE E 369 
 TYR   0.018   0.001   TYR E 613 
 ARG   0.002   0.000   ARG E 219 

*********************** 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
  60 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
REVERT: B  386 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7841 (ptmm)
REVERT: B  409 GLN cc_start: 0.9368 (mt0) cc_final: 0.9097 (mt0)
REVERT: B  424 LYS cc_start: 0.8859 (tptt) cc_final: 0.8395 (tppt)
REVERT: B  444 LYS cc_start: 0.9118 (ptpp) cc_final: 0.8890 (ptpp)
REVERT: B  467 ASP cc_start: 0.8086 (t0) cc_final: 0.7707 (t0)
REVERT: E   62 MET cc_start: 0.9448 (OUTLIER) cc_final: 0.9181 (mtp)
REVERT: E  190 MET cc_start: 0.9233 (ppp) cc_final: 0.8875 (ppp)
REVERT: E  208 GLU cc_start: 0.8794 (tt0) cc_final: 0.8552 (tm-30)
REVERT: E  277 ASN cc_start: 0.9251 (OUTLIER) cc_final: 0.8713 (t0)
REVERT: E  323 MET cc_start: 0.9593 (mmp) cc_final: 0.9277 (mmm)
REVERT: E  366 MET cc_start: 0.8969 (mtp) cc_final: 0.8736 (mtp)
REVERT: E  455 MET cc_start: 0.8921 (ttp) cc_final: 0.8457 (ttt)
REVERT: E  474 MET cc_start: 0.8333 (mmp) cc_final: 0.8088 (mmm)
REVERT: E  498 CYS cc_start: 0.9252 (t) cc_final: 0.8938 (t)
  outliers start: 11
  outliers final: 6
  residues processed: 58
  average time/residue: 0.2045
  time to fit residues: 16.1809
Evaluate side-chains
  56 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  386 LYS
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  435 GLU
Chi-restraints excluded: chain E residue  468 ILE
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 43 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9990
   chunk 47 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 35 optimal weight:    8.9990
   chunk 30 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    1.7388

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.3754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6737  Z= 0.326
  Angle     :  0.572   6.060   9153  Z= 0.296
  Chirality :  0.042   0.143    976
  Planarity :  0.004   0.042   1178
  Dihedral  :  5.261  55.112   1013
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.29 %
    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:  1.39 (0.30), residues: 793
  helix:  1.58 (0.26), residues: 414
  sheet: -0.09 (0.67), residues: 51
  loop :  0.38 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP E 302 
 HIS   0.006   0.001   HIS E  34 
 PHE   0.016   0.002   PHE E 369 
 TYR   0.016   0.002   TYR B 453 
 ARG   0.004   0.000   ARG B 403 

*********************** 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
  64 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
REVERT: B  386 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7971 (ptmm)
REVERT: B  409 GLN cc_start: 0.9337 (mt0) cc_final: 0.9001 (mt0)
REVERT: B  424 LYS cc_start: 0.8905 (tptt) cc_final: 0.8480 (tppt)
REVERT: B  467 ASP cc_start: 0.8110 (t0) cc_final: 0.7774 (t0)
REVERT: E   62 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.9156 (mtp)
REVERT: E  190 MET cc_start: 0.9286 (ppp) cc_final: 0.9080 (ppp)
REVERT: E  208 GLU cc_start: 0.8807 (tt0) cc_final: 0.8574 (tm-30)
REVERT: E  249 MET cc_start: 0.8644 (ttm) cc_final: 0.8043 (mtp)
REVERT: E  270 MET cc_start: 0.8395 (tpt) cc_final: 0.8156 (tpp)
REVERT: E  277 ASN cc_start: 0.9290 (OUTLIER) cc_final: 0.8790 (t0)
REVERT: E  366 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8687 (mtp)
REVERT: E  435 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8738 (mp0)
REVERT: E  455 MET cc_start: 0.8978 (ttp) cc_final: 0.8455 (ttt)
REVERT: E  498 CYS cc_start: 0.9246 (t) cc_final: 0.8928 (t)
  outliers start: 13
  outliers final: 7
  residues processed: 61
  average time/residue: 0.2029
  time to fit residues: 16.8160
Evaluate side-chains
  58 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
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 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  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 14 optimal weight:    0.0670
   chunk 48 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 59 optimal weight:    0.6980
   chunk 69 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   overall best weight:    0.5918

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.3707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6737  Z= 0.168
  Angle     :  0.519  11.617   9153  Z= 0.262
  Chirality :  0.039   0.135    976
  Planarity :  0.004   0.042   1178
  Dihedral  :  4.892  55.788   1013
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.14 %
    Favored  : 85.00 %
  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: 415
  sheet:  0.08 (0.70), residues: 51
  loop :  0.40 (0.35), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 
 PHE   0.012   0.001   PHE E 369 
 TYR   0.013   0.001   TYR B 473 
 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
  63 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  386 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7880 (ptmm)
REVERT: B  409 GLN cc_start: 0.9352 (mt0) cc_final: 0.9062 (mt0)
REVERT: B  424 LYS cc_start: 0.8854 (tptt) cc_final: 0.8437 (tppt)
REVERT: B  467 ASP cc_start: 0.7977 (t0) cc_final: 0.7694 (t0)
REVERT: E   62 MET cc_start: 0.9439 (OUTLIER) cc_final: 0.9173 (mtp)
REVERT: E  190 MET cc_start: 0.9292 (ppp) cc_final: 0.9050 (ppp)
REVERT: E  208 GLU cc_start: 0.8824 (tt0) cc_final: 0.8594 (tm-30)
REVERT: E  249 MET cc_start: 0.8590 (ttm) cc_final: 0.7957 (mtp)
REVERT: E  366 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8717 (mtp)
REVERT: E  455 MET cc_start: 0.8920 (ttp) cc_final: 0.8430 (ttt)
REVERT: E  498 CYS cc_start: 0.9316 (t) cc_final: 0.8811 (t)
  outliers start: 13
  outliers final: 5
  residues processed: 59
  average time/residue: 0.2184
  time to fit residues: 17.4587
Evaluate side-chains
  54 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  366 MET
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  611 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 55 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 64 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0070
   chunk 75 optimal weight:    0.4980
   chunk 45 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   overall best weight:    1.0402

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.3791

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= 0.218
  Angle     :  0.542  10.957   9153  Z= 0.272
  Chirality :  0.040   0.135    976
  Planarity :  0.004   0.042   1178
  Dihedral  :  4.899  55.750   1013
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.57 %
    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:  1.49 (0.30), residues: 793
  helix:  1.63 (0.26), residues: 415
  sheet:  0.13 (0.69), residues: 51
  loop :  0.44 (0.35), residues: 327

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   0.012   0.001   TYR B 473 
 ARG   0.002   0.000   ARG B 403 

*********************** 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
  61 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  386 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7889 (ptmm)
REVERT: B  409 GLN cc_start: 0.9364 (mt0) cc_final: 0.9056 (mt0)
REVERT: B  417 LYS cc_start: 0.9357 (mmmt) cc_final: 0.8858 (mmmt)
REVERT: B  424 LYS cc_start: 0.8875 (tptt) cc_final: 0.8458 (tppt)
REVERT: B  467 ASP cc_start: 0.8019 (t0) cc_final: 0.7749 (t0)
REVERT: E   62 MET cc_start: 0.9441 (OUTLIER) cc_final: 0.9179 (mtp)
REVERT: E  190 MET cc_start: 0.9296 (ppp) cc_final: 0.9079 (ppp)
REVERT: E  208 GLU cc_start: 0.8823 (tt0) cc_final: 0.8577 (tm-30)
REVERT: E  249 MET cc_start: 0.8622 (ttm) cc_final: 0.7945 (mtp)
REVERT: E  366 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8682 (mtp)
REVERT: E  455 MET cc_start: 0.8949 (ttp) cc_final: 0.8444 (ttt)
REVERT: E  498 CYS cc_start: 0.9318 (t) cc_final: 0.8913 (t)
  outliers start: 13
  outliers final: 8
  residues processed: 57
  average time/residue: 0.2218
  time to fit residues: 17.0632
Evaluate side-chains
  58 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
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  513 LEU
Chi-restraints excluded: chain E residue   21 ILE
Chi-restraints excluded: chain E residue   62 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 72 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
E 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.3819

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= 0.193
  Angle     :  0.530  10.483   9153  Z= 0.266
  Chirality :  0.040   0.136    976
  Planarity :  0.004   0.042   1178
  Dihedral  :  4.818  55.896   1013
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 14.00 %
    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:  1.54 (0.30), residues: 793
  helix:  1.66 (0.26), residues: 415
  sheet:  0.19 (0.71), residues: 51
  loop :  0.47 (0.35), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.011   0.001   TYR B 473 
 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
  59 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  386 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7924 (ptmm)
REVERT: B  409 GLN cc_start: 0.9357 (mt0) cc_final: 0.9061 (mt0)
REVERT: B  417 LYS cc_start: 0.9344 (mmmt) cc_final: 0.8847 (mmmt)
REVERT: B  424 LYS cc_start: 0.8862 (tptt) cc_final: 0.8407 (tppt)
REVERT: B  467 ASP cc_start: 0.8063 (t0) cc_final: 0.7799 (t0)
REVERT: E   62 MET cc_start: 0.9442 (OUTLIER) cc_final: 0.9175 (mtp)
REVERT: E  190 MET cc_start: 0.9300 (ppp) cc_final: 0.9086 (ppp)
REVERT: E  208 GLU cc_start: 0.8820 (tt0) cc_final: 0.8571 (tm-30)
REVERT: E  249 MET cc_start: 0.8641 (ttm) cc_final: 0.8106 (mtp)
REVERT: E  366 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8672 (mtp)
REVERT: E  455 MET cc_start: 0.8930 (ttp) cc_final: 0.8441 (ttt)
REVERT: E  498 CYS cc_start: 0.9320 (t) cc_final: 0.8788 (t)
  outliers start: 10
  outliers final: 7
  residues processed: 56
  average time/residue: 0.2127
  time to fit residues: 15.9599
Evaluate side-chains
  57 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  386 LYS
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 62 optimal weight:    0.3980
   chunk 26 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0980
   chunk 71 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.062312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.048707 restraints weight = 26751.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.050600 restraints weight = 13730.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.051871 restraints weight = 8972.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.3845

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= 0.169
  Angle     :  0.525  10.166   9153  Z= 0.262
  Chirality :  0.040   0.141    976
  Planarity :  0.004   0.041   1178
  Dihedral  :  4.747  56.101   1013
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 14.29 %
    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:  1.59 (0.30), residues: 793
  helix:  1.72 (0.26), residues: 415
  sheet:  0.18 (0.71), residues: 51
  loop :  0.47 (0.35), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 
 PHE   0.016   0.001   PHE B 486 
 TYR   0.014   0.001   TYR E  83 
 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: 1549.11 seconds
wall clock time: 28 minutes 35.25 seconds (1715.25 seconds total)