Starting phenix.real_space_refine
on Tue Mar  3 14:58:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yr4_34045/03_2026/7yr4_34045.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yr4_34045/03_2026/7yr4_34045.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yr4_34045/03_2026/7yr4_34045.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yr4_34045/03_2026/7yr4_34045.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yr4_34045/03_2026/7yr4_34045.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yr4_34045/03_2026/7yr4_34045.cif"
  }
  resolution = 4.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.016
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    4103      2.51       5
     N    1064      2.21       5
     O    1190      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6394
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 592, 4832
          Classifications: {'peptide': 592}
          Link IDs: {'PTRANS': 26, 'TRANS': 565}
    Chain: "D"
      Number of atoms: 1562
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1562
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 12, 'TRANS': 182}
  Time building chain proxies: 1.42, per 1000 atoms: 0.22
  Number of scatterers: 6394
  At special positions: 0
  Unit cell: (84.24, 87.36, 118.56, 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    1190      8.00
     N    1064      7.00
     C    4103      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 336 " - pdb=" SG  CYS D 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 379 " - pdb=" SG  CYS D 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 391 " - pdb=" SG  CYS D 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 480 " - pdb=" SG  CYS D 488 " 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
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 249.1 milliseconds
  

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1484

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 4 sheets defined
      51.3% alpha, 4.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.726A  pdb=" N   GLU A  35 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   GLN A  42 " --> pdb=" O   ASP A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 82
    Processing helix  chain 'A' and resid 92 through 101
    Processing helix  chain 'A' and resid 109 through 129
      removed outlier: 3.594A  pdb=" N   SER A 113 " --> pdb=" O   SER A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 155
      removed outlier: 3.994A  pdb=" N   GLU A 150 " --> pdb=" O   PRO A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 193
      removed outlier: 3.665A  pdb=" N   ARG A 161 " --> pdb=" O   ASP A 157 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 4.003A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LEU A 186 " --> pdb=" O   GLU A 182 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLU A 189 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 196
      No H-bonds generated for 'chain 'A' and resid 194 through 196'
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 219 through 252
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 263 through 267
      removed outlier: 3.683A  pdb=" N   LEU A 266 " --> pdb=" O   PRO A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 293 through 299
      removed outlier: 3.650A  pdb=" N   MET A 297 " --> pdb=" O   THR A 294 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   VAL A 298 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 319
      removed outlier: 3.564A  pdb=" N   ALA A 311 " --> pdb=" O   ILE A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 331
      removed outlier: 4.251A  pdb=" N   GLU A 329 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
    Processing helix  chain 'A' and resid 386 through 388
      No H-bonds generated for 'chain 'A' and resid 386 through 388'
    Processing helix  chain 'A' and resid 400 through 412
      removed outlier: 3.800A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   GLU A 406 " --> pdb=" O   GLU A 402 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU A 410 " --> pdb=" O   GLU A 406 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   SER A 411 " --> pdb=" O   ILE A 407 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ALA A 412 " --> pdb=" O   MET A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
      removed outlier: 3.663A  pdb=" N   LEU A 418 " --> pdb=" O   THR A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 447
      removed outlier: 4.174A  pdb=" N   LYS A 441 " --> pdb=" O   ASN A 437 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLN A 442 " --> pdb=" O   PHE A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 466
      removed outlier: 3.992A  pdb=" N   PHE A 452 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 484
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 509
      removed outlier: 4.076A  pdb=" N   SER A 507 " --> pdb=" O   LEU A 503 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ASN A 508 " --> pdb=" O   PHE A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 530
      removed outlier: 3.591A  pdb=" N   TYR A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
    Processing helix  chain 'A' and resid 565 through 572
    Processing helix  chain 'A' and resid 581 through 600
      Proline residue:  A 590  - end of helix
      removed outlier: 4.403A  pdb=" N   TRP A 594 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   LYS A 596 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   ASP A 597 " --> pdb=" O   THR A 593 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 337 through 342
      removed outlier: 3.624A  pdb=" N   VAL D 341 " --> pdb=" O   PRO D 337 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 366 through 371
    Processing helix  chain 'D' and resid 405 through 407
      No H-bonds generated for 'chain 'D' and resid 405 through 407'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 350
    Processing sheet with id=AA2, first strand: chain 'D' and resid 356 through 358
    Processing sheet with id=AA3, first strand: chain 'D' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'D' and resid 473 through 474
      removed outlier: 3.551A  pdb=" N   TYR D 473 " --> pdb=" O   TYR D 489 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   TYR D 489 " --> pdb=" O   TYR D 473 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    272 hydrogen bonds defined for protein.
    795 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.83

  Time building geometry restraints manager: 0.73 seconds

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

  Histogram of bond lengths:
        1.09 -     1.23: 406
        1.23 -     1.38: 2252
        1.38 -     1.53: 3633
        1.53 -     1.68: 229
        1.68 -     1.83: 58
  Bond restraints: 6578
  Sorted by residual:
  bond pdb=" CG  PRO D 373 "
       pdb=" CD  PRO D 373 "
    ideal  model  delta    sigma   weight residual
    1.503  1.085  0.418 3.40e-02 8.65e+02 1.51e+02
  bond pdb=" CB  PRO D 373 "
       pdb=" CG  PRO D 373 "
    ideal  model  delta    sigma   weight residual
    1.492  1.217  0.275 5.00e-02 4.00e+02 3.03e+01
  bond pdb=" N   PRO D 373 "
       pdb=" CD  PRO D 373 "
    ideal  model  delta    sigma   weight residual
    1.473  1.517 -0.044 1.40e-02 5.10e+03 9.86e+00
  bond pdb=" CB  ASN A 601 "
       pdb=" CG  ASN A 601 "
    ideal  model  delta    sigma   weight residual
    1.516  1.562 -0.046 2.50e-02 1.60e+03 3.36e+00
  bond pdb=" CG  LYS D 478 "
       pdb=" CD  LYS D 478 "
    ideal  model  delta    sigma   weight residual
    1.520  1.572 -0.052 3.00e-02 1.11e+03 3.06e+00
  ... (remaining 6573 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     8.18: 8924
        8.18 -    16.36: 11
       16.36 -    24.54: 1
       24.54 -    32.72: 1
       32.72 -    40.90: 1
  Bond angle restraints: 8938
  Sorted by residual:
  angle pdb=" N   PRO D 373 "
        pdb=" CD  PRO D 373 "
        pdb=" CG  PRO D 373 "
      ideal   model   delta    sigma   weight residual
     103.20   75.60   27.60 1.50e+00 4.44e-01 3.39e+02
  angle pdb=" CB  PRO D 373 "
        pdb=" CG  PRO D 373 "
        pdb=" CD  PRO D 373 "
      ideal   model   delta    sigma   weight residual
     106.10  147.00  -40.90 3.20e+00 9.77e-02 1.63e+02
  angle pdb=" CA  PRO D 373 "
        pdb=" CB  PRO D 373 "
        pdb=" CG  PRO D 373 "
      ideal   model   delta    sigma   weight residual
     104.50   80.22   24.28 1.90e+00 2.77e-01 1.63e+02
  angle pdb=" CA  PRO D 373 "
        pdb=" N   PRO D 373 "
        pdb=" CD  PRO D 373 "
      ideal   model   delta    sigma   weight residual
     112.00  103.00    9.00 1.40e+00 5.10e-01 4.13e+01
  angle pdb=" C   LYS A 600 "
        pdb=" N   ASN A 601 "
        pdb=" CA  ASN A 601 "
      ideal   model   delta    sigma   weight residual
     123.05  130.49   -7.44 1.57e+00 4.06e-01 2.25e+01
  ... (remaining 8933 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 3445
       17.77 -    35.55: 354
       35.55 -    53.32: 58
       53.32 -    71.09: 15
       71.09 -    88.86: 10
  Dihedral angle restraints: 3882
    sinusoidal: 1571
      harmonic: 2311
  Sorted by residual:
  dihedral pdb=" CB  CYS A 133 "
           pdb=" SG  CYS A 133 "
           pdb=" SG  CYS A 141 "
           pdb=" CB  CYS A 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   19.27   73.73     1      1.00e+01 1.00e-02 6.91e+01
  dihedral pdb=" CB  CYS D 336 "
           pdb=" SG  CYS D 336 "
           pdb=" SG  CYS D 361 "
           pdb=" CB  CYS D 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   19.50   73.50     1      1.00e+01 1.00e-02 6.87e+01
  dihedral pdb=" CB  CYS D 391 "
           pdb=" SG  CYS D 391 "
           pdb=" SG  CYS D 525 "
           pdb=" CB  CYS D 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -146.07   60.07     1      1.00e+01 1.00e-02 4.81e+01
  ... (remaining 3879 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 741
       0.063 -    0.126: 159
       0.126 -    0.189: 28
       0.189 -    0.252: 2
       0.252 -    0.315: 1
  Chirality restraints: 931
  Sorted by residual:
  chirality pdb=" CB  VAL A 293 "
            pdb=" CA  VAL A 293 "
            pdb=" CG1 VAL A 293 "
            pdb=" CG2 VAL A 293 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.49e+00
  chirality pdb=" CA  ASN A 601 "
            pdb=" N   ASN A 601 "
            pdb=" C   ASN A 601 "
            pdb=" CB  ASN A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CB  VAL A 364 "
            pdb=" CA  VAL A 364 "
            pdb=" CG1 VAL A 364 "
            pdb=" CG2 VAL A 364 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 928 not shown)

  Planarity restraints: 1159
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 477 "    0.031 2.00e-02 2.50e+03   3.06e-02 2.35e+01
        pdb=" CG  TRP A 477 "   -0.082 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 477 "    0.040 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 477 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 477 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 477 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 477 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 477 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 477 "    0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 477 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 288 "    0.062 5.00e-02 4.00e+02   9.48e-02 1.44e+01
        pdb=" N   PRO A 289 "   -0.164 5.00e-02 4.00e+02
        pdb=" CA  PRO A 289 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO A 289 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 459 "   -0.017 2.00e-02 2.50e+03   2.25e-02 1.26e+01
        pdb=" CG  TRP A 459 "    0.061 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 459 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 459 "   -0.013 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 459 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 459 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 459 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 459 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 459 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 459 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1156 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 961
        2.76 -     3.29: 6316
        3.29 -     3.83: 10623
        3.83 -     4.36: 12003
        4.36 -     4.90: 19898
  Nonbonded interactions: 49801
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 278 "
            pdb=" OG1 THR A 282 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OH  TYR A  83 "
            pdb=" OH  TYR D 489 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   SER A 105 "
            pdb=" OG  SER A 113 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   HIS A 239 "
            pdb=" ND2 ASN A 599 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" O   THR D 393 "
            pdb=" OG1 THR D 523 "
     model   vdw
     2.322 3.040
  ... (remaining 49796 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:             2.830
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.800
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5610
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      :  0.008   0.418   6585  Z= 0.282
  Angle     :  1.166  40.904   8952  Z= 0.600
  Chirality :  0.055   0.315    931
  Planarity :  0.007   0.095   1159
  Dihedral  : 14.906  88.862   2377
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.40 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.79 (0.27), residues: 783
  helix: -0.62 (0.25), residues: 350
  sheet: -1.30 (0.76), residues: 32
  loop : -1.68 (0.28), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 219 
 TYR   0.030   0.003   TYR A 279 
 PHE   0.035   0.003   PHE D 497 
 TRP   0.082   0.004   TRP A 477 
 HIS   0.005   0.001   HIS D 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00776 ( 6578)
  covalent geometry    : angle       1.16486 ( 8938)
  SS BOND              : bond        0.00516 (    7)
  SS BOND              : angle       1.78588 (   14)
  hydrogen bonds       : bond        0.10658 (  272)
  hydrogen bonds       : angle       6.01419 (  795)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 270
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  391 LEU cc_start: 0.7872 (tp) cc_final: 0.7667 (tp)
REVERT: A  410 LEU cc_start: 0.7503 (mt) cc_final: 0.6806 (mt)
REVERT: A  441 LYS cc_start: 0.7267 (tmtt) cc_final: 0.7056 (tptm)
REVERT: A  520 LEU cc_start: 0.6720 (mp) cc_final: 0.6245 (tt)
REVERT: A  523 PHE cc_start: 0.6854 (m-80) cc_final: 0.6539 (m-80)
REVERT: A  587 TYR cc_start: 0.5147 (t80) cc_final: 0.4711 (t80)
REVERT: A  592 PHE cc_start: 0.4417 (t80) cc_final: 0.3238 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 270
  average time/residue: 0.0905
  time to fit residues: 30.8306
Evaluate side-chains
  150 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0050
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.7794

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.100517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.079203 restraints weight = 26435.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.081750 restraints weight = 19216.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.083664 restraints weight = 14971.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.085131 restraints weight = 12267.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.086311 restraints weight = 10427.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.3818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6585  Z= 0.144
  Angle     :  0.689   9.426   8952  Z= 0.349
  Chirality :  0.044   0.212    931
  Planarity :  0.006   0.064   1159
  Dihedral  :  5.663  29.126    854
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.28), residues: 783
  helix: -0.10 (0.26), residues: 362
  sheet: -0.92 (0.76), residues: 33
  loop : -1.42 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 346 
 TYR   0.022   0.002   TYR A 385 
 PHE   0.023   0.002   PHE A 525 
 TRP   0.026   0.002   TRP A 473 
 HIS   0.006   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6578)
  covalent geometry    : angle       0.68365 ( 8938)
  SS BOND              : bond        0.00341 (    7)
  SS BOND              : angle       2.22390 (   14)
  hydrogen bonds       : bond        0.04445 (  272)
  hydrogen bonds       : angle       5.04391 (  795)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  216 ASP cc_start: 0.8847 (m-30) cc_final: 0.8596 (m-30)
REVERT: A  277 ASN cc_start: 0.9307 (m110) cc_final: 0.8740 (t0)
REVERT: A  315 PHE cc_start: 0.9489 (m-10) cc_final: 0.8643 (m-10)
REVERT: A  355 ASP cc_start: 0.8305 (t0) cc_final: 0.7863 (t0)
REVERT: A  359 LEU cc_start: 0.9479 (tp) cc_final: 0.9266 (tp)
REVERT: A  376 MET cc_start: 0.9377 (tpt) cc_final: 0.8619 (tpt)
REVERT: A  379 ILE cc_start: 0.9520 (mm) cc_final: 0.9263 (mm)
REVERT: A  380 GLN cc_start: 0.9583 (tp40) cc_final: 0.9310 (tp40)
REVERT: A  407 ILE cc_start: 0.8981 (mt) cc_final: 0.8679 (mt)
REVERT: A  441 LYS cc_start: 0.8610 (tmtt) cc_final: 0.8059 (tptt)
REVERT: A  455 MET cc_start: 0.8716 (ppp) cc_final: 0.8145 (ppp)
REVERT: A  480 MET cc_start: 0.9148 (tpt) cc_final: 0.8714 (tpt)
REVERT: A  520 LEU cc_start: 0.9375 (mp) cc_final: 0.9150 (tt)
REVERT: A  523 PHE cc_start: 0.9356 (m-80) cc_final: 0.9072 (m-80)
REVERT: A  525 PHE cc_start: 0.9425 (m-80) cc_final: 0.8677 (m-80)
REVERT: A  554 LEU cc_start: 0.9290 (tp) cc_final: 0.9069 (tp)
REVERT: A  564 GLU cc_start: 0.9166 (mp0) cc_final: 0.8746 (mp0)
REVERT: A  587 TYR cc_start: 0.8894 (t80) cc_final: 0.7384 (t80)
REVERT: D  378 LYS cc_start: 0.9006 (tmtt) cc_final: 0.8499 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 189
  average time/residue: 0.0831
  time to fit residues: 20.4353
Evaluate side-chains
  139 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 13 optimal weight:    0.4980
   chunk 31 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 68 optimal weight:   30.0000
   chunk 20 optimal weight:    9.9990
   chunk 40 optimal weight:    0.1980
   chunk 27 optimal weight:    0.1980
   chunk 53 optimal weight:    2.9990
   chunk 59 optimal weight:    9.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 239 HIS
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 HIS
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 556 ASN
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.099782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.079312 restraints weight = 26180.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.081788 restraints weight = 18877.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.083627 restraints weight = 14664.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.085095 restraints weight = 11957.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.086231 restraints weight = 10085.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.4711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6585  Z= 0.130
  Angle     :  0.655   9.652   8952  Z= 0.332
  Chirality :  0.043   0.147    931
  Planarity :  0.005   0.051   1159
  Dihedral  :  5.157  26.342    854
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 14.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.83 (0.29), residues: 783
  helix:  0.23 (0.27), residues: 357
  sheet: -0.78 (0.79), residues: 33
  loop : -1.26 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 306 
 TYR   0.017   0.002   TYR D 495 
 PHE   0.018   0.001   PHE A 356 
 TRP   0.023   0.002   TRP A 459 
 HIS   0.006   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 6578)
  covalent geometry    : angle       0.64886 ( 8938)
  SS BOND              : bond        0.00698 (    7)
  SS BOND              : angle       2.32318 (   14)
  hydrogen bonds       : bond        0.04151 (  272)
  hydrogen bonds       : angle       4.95661 (  795)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 LEU cc_start: 0.9678 (mt) cc_final: 0.9421 (mt)
REVERT: A  207 TYR cc_start: 0.9329 (m-80) cc_final: 0.8650 (m-80)
REVERT: A  212 VAL cc_start: 0.8651 (m) cc_final: 0.8421 (p)
REVERT: A  277 ASN cc_start: 0.9321 (m110) cc_final: 0.8762 (t0)
REVERT: A  315 PHE cc_start: 0.9434 (m-10) cc_final: 0.8405 (m-10)
REVERT: A  355 ASP cc_start: 0.8150 (t0) cc_final: 0.7767 (t0)
REVERT: A  376 MET cc_start: 0.9404 (tpt) cc_final: 0.8631 (tpt)
REVERT: A  379 ILE cc_start: 0.9581 (mm) cc_final: 0.9264 (mm)
REVERT: A  380 GLN cc_start: 0.9589 (tp40) cc_final: 0.9306 (tp40)
REVERT: A  417 HIS cc_start: 0.9109 (t-90) cc_final: 0.8901 (t-170)
REVERT: A  441 LYS cc_start: 0.8614 (tmtt) cc_final: 0.8133 (tptt)
REVERT: A  455 MET cc_start: 0.8554 (ppp) cc_final: 0.7963 (ppp)
REVERT: A  480 MET cc_start: 0.8955 (tpt) cc_final: 0.8644 (tpt)
REVERT: A  512 PHE cc_start: 0.8282 (m-10) cc_final: 0.7720 (m-10)
REVERT: A  513 ILE cc_start: 0.9566 (mm) cc_final: 0.9267 (mm)
REVERT: A  519 THR cc_start: 0.9705 (p) cc_final: 0.9331 (p)
REVERT: A  520 LEU cc_start: 0.9431 (mp) cc_final: 0.9227 (tt)
REVERT: A  523 PHE cc_start: 0.9386 (m-80) cc_final: 0.8619 (m-80)
REVERT: A  525 PHE cc_start: 0.9387 (m-80) cc_final: 0.8916 (m-80)
REVERT: A  554 LEU cc_start: 0.9266 (tp) cc_final: 0.9030 (tp)
REVERT: A  564 GLU cc_start: 0.9144 (mp0) cc_final: 0.8723 (mp0)
REVERT: A  587 TYR cc_start: 0.8997 (t80) cc_final: 0.7936 (t80)
REVERT: A  588 PHE cc_start: 0.9043 (m-80) cc_final: 0.8153 (m-80)
REVERT: D  346 ARG cc_start: 0.8856 (tpt90) cc_final: 0.8571 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.0825
  time to fit residues: 19.0647
Evaluate side-chains
  143 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 17 optimal weight:    7.9990
   chunk 20 optimal weight:    8.9990
   chunk 15 optimal weight:   10.0000
   chunk 65 optimal weight:    4.9990
   chunk 73 optimal weight:    0.0770
   chunk 64 optimal weight:    0.0370
   chunk 11 optimal weight:    8.9990
   chunk 19 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   overall best weight:    1.9820

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

Flipped N/Q/H residues before XYZ refinement:
A  64 ASN
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 437 ASN
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 343 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.093695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.074610 restraints weight = 26899.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.077192 restraints weight = 18702.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.079104 restraints weight = 14091.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.080600 restraints weight = 11248.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.081714 restraints weight = 9356.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.5373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6585  Z= 0.146
  Angle     :  0.641   9.450   8952  Z= 0.329
  Chirality :  0.043   0.148    931
  Planarity :  0.005   0.044   1159
  Dihedral  :  5.002  25.786    854
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 15.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.29), residues: 783
  helix:  0.28 (0.27), residues: 363
  sheet: -0.60 (0.82), residues: 33
  loop : -1.20 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 582 
 TYR   0.026   0.002   TYR A 515 
 PHE   0.020   0.002   PHE A 356 
 TRP   0.036   0.002   TRP A 461 
 HIS   0.006   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6578)
  covalent geometry    : angle       0.63800 ( 8938)
  SS BOND              : bond        0.00673 (    7)
  SS BOND              : angle       1.61507 (   14)
  hydrogen bonds       : bond        0.04090 (  272)
  hydrogen bonds       : angle       4.88651 (  795)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 LEU cc_start: 0.9653 (mt) cc_final: 0.9349 (mt)
REVERT: A  177 ARG cc_start: 0.8572 (ptp90) cc_final: 0.8148 (ptt90)
REVERT: A  207 TYR cc_start: 0.9352 (m-80) cc_final: 0.8760 (m-80)
REVERT: A  227 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8818 (mm-30)
REVERT: A  237 TYR cc_start: 0.8536 (t80) cc_final: 0.8301 (t80)
REVERT: A  273 ARG cc_start: 0.7509 (ttt-90) cc_final: 0.6894 (ptp-170)
REVERT: A  277 ASN cc_start: 0.9333 (m110) cc_final: 0.8764 (t0)
REVERT: A  315 PHE cc_start: 0.9442 (m-10) cc_final: 0.8527 (m-10)
REVERT: A  355 ASP cc_start: 0.8476 (t0) cc_final: 0.7924 (t0)
REVERT: A  376 MET cc_start: 0.9335 (tpt) cc_final: 0.8588 (tpt)
REVERT: A  379 ILE cc_start: 0.9572 (mm) cc_final: 0.9291 (mm)
REVERT: A  380 GLN cc_start: 0.9569 (tp40) cc_final: 0.9303 (tp-100)
REVERT: A  417 HIS cc_start: 0.9210 (t-90) cc_final: 0.8998 (t-170)
REVERT: A  441 LYS cc_start: 0.8610 (tmtt) cc_final: 0.8168 (tptt)
REVERT: A  455 MET cc_start: 0.8512 (ppp) cc_final: 0.7765 (ppp)
REVERT: A  480 MET cc_start: 0.8920 (tpt) cc_final: 0.8634 (tpt)
REVERT: A  505 HIS cc_start: 0.8550 (m90) cc_final: 0.8186 (m90)
REVERT: A  512 PHE cc_start: 0.8419 (m-10) cc_final: 0.7770 (m-80)
REVERT: A  515 TYR cc_start: 0.8197 (m-10) cc_final: 0.7859 (m-80)
REVERT: A  516 TYR cc_start: 0.8574 (t80) cc_final: 0.8121 (t80)
REVERT: A  519 THR cc_start: 0.9721 (p) cc_final: 0.9485 (p)
REVERT: A  523 PHE cc_start: 0.9296 (m-80) cc_final: 0.8907 (m-80)
REVERT: A  525 PHE cc_start: 0.9448 (m-80) cc_final: 0.9094 (m-80)
REVERT: A  554 LEU cc_start: 0.9270 (tp) cc_final: 0.9007 (tp)
REVERT: A  564 GLU cc_start: 0.9056 (mp0) cc_final: 0.8679 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.0801
  time to fit residues: 18.1440
Evaluate side-chains
  141 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 47 optimal weight:    8.9990
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:   30.0000
   chunk 77 optimal weight:    0.5980
   chunk 64 optimal weight:    0.5980
   chunk 20 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 HIS
A 345 HIS
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 HIS
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 370 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.094033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.074462 restraints weight = 27047.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.076980 restraints weight = 18874.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.078935 restraints weight = 14329.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.080362 restraints weight = 11476.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.081550 restraints weight = 9628.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.5677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6585  Z= 0.119
  Angle     :  0.625   6.904   8952  Z= 0.316
  Chirality :  0.043   0.148    931
  Planarity :  0.004   0.042   1159
  Dihedral  :  4.876  24.356    854
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.30), residues: 783
  helix:  0.64 (0.28), residues: 353
  sheet: -0.39 (0.84), residues: 33
  loop : -1.03 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 457 
 TYR   0.018   0.001   TYR D 495 
 PHE   0.018   0.002   PHE A 356 
 TRP   0.029   0.001   TRP A 461 
 HIS   0.005   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6578)
  covalent geometry    : angle       0.62088 ( 8938)
  SS BOND              : bond        0.00225 (    7)
  SS BOND              : angle       1.89112 (   14)
  hydrogen bonds       : bond        0.03930 (  272)
  hydrogen bonds       : angle       4.86812 (  795)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 GLN cc_start: 0.7903 (mp10) cc_final: 0.7601 (mp10)
REVERT: A  207 TYR cc_start: 0.9293 (m-80) cc_final: 0.8683 (m-80)
REVERT: A  209 VAL cc_start: 0.9124 (t) cc_final: 0.8658 (t)
REVERT: A  215 TYR cc_start: 0.8628 (m-80) cc_final: 0.8298 (m-80)
REVERT: A  227 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8753 (mm-30)
REVERT: A  315 PHE cc_start: 0.9430 (m-10) cc_final: 0.8173 (m-10)
REVERT: A  355 ASP cc_start: 0.8384 (t0) cc_final: 0.7800 (t0)
REVERT: A  376 MET cc_start: 0.9378 (tpt) cc_final: 0.8526 (tpt)
REVERT: A  379 ILE cc_start: 0.9550 (mm) cc_final: 0.9293 (mm)
REVERT: A  380 GLN cc_start: 0.9552 (tp40) cc_final: 0.9322 (tp40)
REVERT: A  441 LYS cc_start: 0.8666 (tmtt) cc_final: 0.8298 (tptt)
REVERT: A  455 MET cc_start: 0.8533 (ppp) cc_final: 0.7860 (ppp)
REVERT: A  461 TRP cc_start: 0.8340 (m-10) cc_final: 0.8027 (m-90)
REVERT: A  480 MET cc_start: 0.8908 (tpt) cc_final: 0.8597 (tpt)
REVERT: A  505 HIS cc_start: 0.8564 (m90) cc_final: 0.8213 (m90)
REVERT: A  512 PHE cc_start: 0.8342 (m-10) cc_final: 0.7650 (m-10)
REVERT: A  515 TYR cc_start: 0.8286 (m-10) cc_final: 0.7921 (m-80)
REVERT: A  516 TYR cc_start: 0.8644 (t80) cc_final: 0.8274 (t80)
REVERT: A  519 THR cc_start: 0.9679 (p) cc_final: 0.9477 (p)
REVERT: A  523 PHE cc_start: 0.9516 (m-80) cc_final: 0.9130 (m-80)
REVERT: A  525 PHE cc_start: 0.9527 (m-80) cc_final: 0.9067 (m-80)
REVERT: A  554 LEU cc_start: 0.9242 (tp) cc_final: 0.8979 (tp)
REVERT: A  564 GLU cc_start: 0.9028 (mp0) cc_final: 0.8609 (mp0)
REVERT: D  444 LYS cc_start: 0.9562 (ttmt) cc_final: 0.9291 (ttmm)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.0781
  time to fit residues: 16.8439
Evaluate side-chains
  141 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    0.2980
   chunk 29 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 39 optimal weight:   10.0000
   chunk 24 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 1 optimal weight:   10.0000
   chunk 8 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 HIS
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.094472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.074484 restraints weight = 27606.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.076831 restraints weight = 19839.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.078666 restraints weight = 15381.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.080087 restraints weight = 12499.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.081212 restraints weight = 10514.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.6008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6585  Z= 0.121
  Angle     :  0.627   7.262   8952  Z= 0.318
  Chirality :  0.043   0.170    931
  Planarity :  0.004   0.039   1159
  Dihedral  :  4.782  20.973    854
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.30), residues: 783
  helix:  0.55 (0.28), residues: 358
  sheet: -0.27 (0.83), residues: 33
  loop : -1.01 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG A 177 
 TYR   0.012   0.001   TYR A 516 
 PHE   0.018   0.001   PHE A 356 
 TRP   0.062   0.002   TRP A 163 
 HIS   0.005   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6578)
  covalent geometry    : angle       0.62607 ( 8938)
  SS BOND              : bond        0.00361 (    7)
  SS BOND              : angle       1.20044 (   14)
  hydrogen bonds       : bond        0.03946 (  272)
  hydrogen bonds       : angle       4.84293 (  795)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.8268 (ppp) cc_final: 0.7888 (ppp)
REVERT: A   89 GLN cc_start: 0.7498 (mp10) cc_final: 0.6824 (mp10)
REVERT: A   94 LYS cc_start: 0.9465 (pttp) cc_final: 0.9214 (pttp)
REVERT: A  207 TYR cc_start: 0.9324 (m-80) cc_final: 0.8962 (m-80)
REVERT: A  215 TYR cc_start: 0.8604 (m-80) cc_final: 0.8299 (m-80)
REVERT: A  227 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8742 (mm-30)
REVERT: A  237 TYR cc_start: 0.8528 (t80) cc_final: 0.8310 (t80)
REVERT: A  315 PHE cc_start: 0.9417 (m-10) cc_final: 0.8020 (m-10)
REVERT: A  323 MET cc_start: 0.6540 (tmm) cc_final: 0.6301 (tmm)
REVERT: A  355 ASP cc_start: 0.8337 (t0) cc_final: 0.7793 (t0)
REVERT: A  376 MET cc_start: 0.9409 (tpt) cc_final: 0.8670 (tpt)
REVERT: A  379 ILE cc_start: 0.9533 (mm) cc_final: 0.9301 (mm)
REVERT: A  380 GLN cc_start: 0.9551 (tp40) cc_final: 0.9348 (tp40)
REVERT: A  441 LYS cc_start: 0.8622 (tmtt) cc_final: 0.8257 (tptt)
REVERT: A  455 MET cc_start: 0.8525 (ppp) cc_final: 0.7840 (ppp)
REVERT: A  461 TRP cc_start: 0.8438 (m-10) cc_final: 0.8171 (m-90)
REVERT: A  480 MET cc_start: 0.8956 (tpt) cc_final: 0.8627 (tpt)
REVERT: A  505 HIS cc_start: 0.8569 (m90) cc_final: 0.8210 (m90)
REVERT: A  512 PHE cc_start: 0.8390 (m-10) cc_final: 0.7720 (m-10)
REVERT: A  515 TYR cc_start: 0.8352 (m-10) cc_final: 0.7985 (m-80)
REVERT: A  516 TYR cc_start: 0.8680 (t80) cc_final: 0.8312 (t80)
REVERT: A  519 THR cc_start: 0.9671 (p) cc_final: 0.9448 (p)
REVERT: A  523 PHE cc_start: 0.9567 (m-80) cc_final: 0.9111 (m-80)
REVERT: A  525 PHE cc_start: 0.9511 (m-80) cc_final: 0.9099 (m-80)
REVERT: A  554 LEU cc_start: 0.9179 (tp) cc_final: 0.8915 (tp)
REVERT: A  564 GLU cc_start: 0.8977 (mp0) cc_final: 0.8633 (mp0)
REVERT: A  591 LEU cc_start: 0.9209 (mt) cc_final: 0.8802 (mt)
REVERT: D  417 ASN cc_start: 0.9385 (p0) cc_final: 0.9155 (p0)
REVERT: D  444 LYS cc_start: 0.9553 (ttmt) cc_final: 0.9289 (ttmm)
REVERT: D  471 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8096 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.0823
  time to fit residues: 18.1662
Evaluate side-chains
  141 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 31 optimal weight:    8.9990
   chunk 46 optimal weight:    0.6980
   chunk 64 optimal weight:    9.9990
   chunk 58 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 30 optimal weight:    8.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 380 GLN
A 535 HIS
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 599 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.089142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.070773 restraints weight = 28527.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.073131 restraints weight = 19963.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.074947 restraints weight = 15157.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.076357 restraints weight = 12087.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.077457 restraints weight = 10041.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.6576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6585  Z= 0.187
  Angle     :  0.681   7.056   8952  Z= 0.355
  Chirality :  0.044   0.180    931
  Planarity :  0.005   0.043   1159
  Dihedral  :  5.050  22.647    854
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 18.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.60 %
    Favored  : 97.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.29), residues: 783
  helix:  0.34 (0.27), residues: 369
  sheet: -0.36 (0.80), residues: 34
  loop : -1.22 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 177 
 TYR   0.015   0.002   TYR A 237 
 PHE   0.012   0.002   PHE A 400 
 TRP   0.026   0.002   TRP A 203 
 HIS   0.007   0.002   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 6578)
  covalent geometry    : angle       0.68016 ( 8938)
  SS BOND              : bond        0.00307 (    7)
  SS BOND              : angle       1.16898 (   14)
  hydrogen bonds       : bond        0.04070 (  272)
  hydrogen bonds       : angle       5.13886 (  795)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 162
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.8185 (ppp) cc_final: 0.7942 (ppp)
REVERT: A   89 GLN cc_start: 0.7542 (mp10) cc_final: 0.7142 (mp10)
REVERT: A   94 LYS cc_start: 0.9452 (pttp) cc_final: 0.9098 (pttp)
REVERT: A  207 TYR cc_start: 0.9370 (m-80) cc_final: 0.8937 (m-80)
REVERT: A  209 VAL cc_start: 0.9201 (t) cc_final: 0.8804 (t)
REVERT: A  227 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8586 (mm-30)
REVERT: A  237 TYR cc_start: 0.8601 (t80) cc_final: 0.8271 (t80)
REVERT: A  315 PHE cc_start: 0.9483 (m-10) cc_final: 0.8479 (m-10)
REVERT: A  355 ASP cc_start: 0.8791 (t0) cc_final: 0.8363 (t0)
REVERT: A  376 MET cc_start: 0.9373 (tpt) cc_final: 0.8744 (tpt)
REVERT: A  379 ILE cc_start: 0.9498 (mm) cc_final: 0.9251 (mm)
REVERT: A  441 LYS cc_start: 0.8712 (tmtt) cc_final: 0.8373 (tptt)
REVERT: A  461 TRP cc_start: 0.8625 (m-10) cc_final: 0.8054 (m-90)
REVERT: A  480 MET cc_start: 0.8881 (tpt) cc_final: 0.8519 (tpt)
REVERT: A  505 HIS cc_start: 0.8711 (m90) cc_final: 0.8274 (m90)
REVERT: A  512 PHE cc_start: 0.8522 (m-10) cc_final: 0.7887 (m-10)
REVERT: A  516 TYR cc_start: 0.8726 (t80) cc_final: 0.8263 (t80)
REVERT: A  518 ARG cc_start: 0.8856 (ptt90) cc_final: 0.8505 (mtt90)
REVERT: A  519 THR cc_start: 0.9709 (p) cc_final: 0.9491 (p)
REVERT: A  523 PHE cc_start: 0.9503 (m-80) cc_final: 0.9052 (m-80)
REVERT: A  525 PHE cc_start: 0.9530 (m-80) cc_final: 0.9120 (m-80)
REVERT: A  554 LEU cc_start: 0.9255 (tp) cc_final: 0.8988 (tp)
REVERT: A  564 GLU cc_start: 0.9089 (mp0) cc_final: 0.8654 (mp0)
REVERT: A  588 PHE cc_start: 0.9153 (m-80) cc_final: 0.8930 (m-80)
REVERT: D  444 LYS cc_start: 0.9547 (ttmt) cc_final: 0.9300 (ttmt)
  outliers start: 1
  outliers final: 0
  residues processed: 163
  average time/residue: 0.0817
  time to fit residues: 17.5291
Evaluate side-chains
  138 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 70 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 53 optimal weight:    0.7980
   chunk 49 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 54 optimal weight:    0.4980
   chunk 66 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 300 GLN
A 330 ASN
A 535 HIS
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.092437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.073174 restraints weight = 27731.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.075562 restraints weight = 19683.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.077365 restraints weight = 15133.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.078804 restraints weight = 12261.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.079917 restraints weight = 10280.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.6751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6585  Z= 0.128
  Angle     :  0.653   6.662   8952  Z= 0.335
  Chirality :  0.045   0.199    931
  Planarity :  0.004   0.037   1159
  Dihedral  :  4.892  20.999    854
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.29), residues: 783
  helix:  0.41 (0.27), residues: 367
  sheet: -0.20 (0.82), residues: 34
  loop : -1.17 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 177 
 TYR   0.013   0.001   TYR A 516 
 PHE   0.012   0.001   PHE A 230 
 TRP   0.025   0.002   TRP A 203 
 HIS   0.007   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 6578)
  covalent geometry    : angle       0.65252 ( 8938)
  SS BOND              : bond        0.00296 (    7)
  SS BOND              : angle       0.88560 (   14)
  hydrogen bonds       : bond        0.03999 (  272)
  hydrogen bonds       : angle       5.11723 (  795)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.9542 (ppp) cc_final: 0.9319 (ppp)
REVERT: A   82 MET cc_start: 0.8272 (ppp) cc_final: 0.8058 (ppp)
REVERT: A   89 GLN cc_start: 0.7545 (mp10) cc_final: 0.7097 (mp10)
REVERT: A   94 LYS cc_start: 0.9435 (pttp) cc_final: 0.9114 (pttp)
REVERT: A  154 ASN cc_start: 0.8695 (m-40) cc_final: 0.8492 (m-40)
REVERT: A  176 LEU cc_start: 0.8204 (mm) cc_final: 0.7624 (mm)
REVERT: A  215 TYR cc_start: 0.8867 (m-80) cc_final: 0.8390 (m-80)
REVERT: A  227 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8601 (mm-30)
REVERT: A  237 TYR cc_start: 0.8543 (t80) cc_final: 0.8224 (t80)
REVERT: A  315 PHE cc_start: 0.9570 (m-10) cc_final: 0.8427 (m-10)
REVERT: A  355 ASP cc_start: 0.8872 (t0) cc_final: 0.8531 (t0)
REVERT: A  376 MET cc_start: 0.9394 (tpt) cc_final: 0.8722 (tpt)
REVERT: A  417 HIS cc_start: 0.9484 (t-170) cc_final: 0.9254 (t-170)
REVERT: A  441 LYS cc_start: 0.8699 (tmtt) cc_final: 0.8327 (tptt)
REVERT: A  455 MET cc_start: 0.8609 (ppp) cc_final: 0.7907 (ppp)
REVERT: A  461 TRP cc_start: 0.8618 (m-10) cc_final: 0.8260 (m-90)
REVERT: A  480 MET cc_start: 0.8877 (tpt) cc_final: 0.8486 (tpt)
REVERT: A  505 HIS cc_start: 0.8658 (m90) cc_final: 0.8187 (m90)
REVERT: A  512 PHE cc_start: 0.8297 (m-10) cc_final: 0.7402 (m-10)
REVERT: A  515 TYR cc_start: 0.8165 (m-10) cc_final: 0.7936 (m-80)
REVERT: A  516 TYR cc_start: 0.8645 (t80) cc_final: 0.8200 (t80)
REVERT: A  523 PHE cc_start: 0.9490 (m-80) cc_final: 0.8994 (m-80)
REVERT: A  525 PHE cc_start: 0.9490 (m-80) cc_final: 0.9126 (m-80)
REVERT: A  554 LEU cc_start: 0.9241 (tp) cc_final: 0.8968 (tp)
REVERT: A  564 GLU cc_start: 0.9014 (mp0) cc_final: 0.8580 (mp0)
REVERT: A  588 PHE cc_start: 0.9023 (m-80) cc_final: 0.8787 (m-80)
REVERT: D  386 LYS cc_start: 0.8925 (pttp) cc_final: 0.8469 (pttm)
REVERT: D  444 LYS cc_start: 0.9566 (ttmt) cc_final: 0.9320 (ttmt)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.0744
  time to fit residues: 16.1710
Evaluate side-chains
  143 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 26 optimal weight:    0.0570
   chunk 3 optimal weight:   10.0000
   chunk 22 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 30 optimal weight:   10.0000
   chunk 1 optimal weight:   10.0000
   chunk 24 optimal weight:    0.0370
   chunk 2 optimal weight:    1.9990
   chunk 73 optimal weight:    0.0000
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 HIS
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.093803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.073902 restraints weight = 26763.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.076339 restraints weight = 19066.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.078222 restraints weight = 14721.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.079719 restraints weight = 11948.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.080858 restraints weight = 10008.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.6998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6585  Z= 0.131
  Angle     :  0.675   6.792   8952  Z= 0.351
  Chirality :  0.046   0.213    931
  Planarity :  0.004   0.038   1159
  Dihedral  :  4.898  23.145    854
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.30), residues: 783
  helix:  0.33 (0.27), residues: 372
  sheet: -1.16 (0.73), residues: 44
  loop : -1.10 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 306 
 TYR   0.014   0.001   TYR A 497 
 PHE   0.027   0.001   PHE A 356 
 TRP   0.031   0.002   TRP A 302 
 HIS   0.008   0.002   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6578)
  covalent geometry    : angle       0.67535 ( 8938)
  SS BOND              : bond        0.00246 (    7)
  SS BOND              : angle       0.75931 (   14)
  hydrogen bonds       : bond        0.04153 (  272)
  hydrogen bonds       : angle       5.21744 (  795)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.9536 (ppp) cc_final: 0.9307 (ppp)
REVERT: A   82 MET cc_start: 0.8217 (ppp) cc_final: 0.7945 (ppp)
REVERT: A   85 LEU cc_start: 0.9378 (pt) cc_final: 0.9144 (tp)
REVERT: A   94 LYS cc_start: 0.9403 (pttp) cc_final: 0.9075 (pttp)
REVERT: A   97 LEU cc_start: 0.9575 (mt) cc_final: 0.9362 (mt)
REVERT: A  176 LEU cc_start: 0.8145 (mm) cc_final: 0.7548 (mm)
REVERT: A  207 TYR cc_start: 0.9372 (m-80) cc_final: 0.8915 (m-80)
REVERT: A  215 TYR cc_start: 0.8859 (m-80) cc_final: 0.8368 (m-80)
REVERT: A  227 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8655 (mm-30)
REVERT: A  237 TYR cc_start: 0.8487 (t80) cc_final: 0.8236 (t80)
REVERT: A  270 MET cc_start: 0.8833 (tpp) cc_final: 0.7989 (tpp)
REVERT: A  315 PHE cc_start: 0.9510 (m-10) cc_final: 0.8203 (m-10)
REVERT: A  355 ASP cc_start: 0.8454 (t0) cc_final: 0.8164 (t0)
REVERT: A  376 MET cc_start: 0.9417 (tpt) cc_final: 0.8705 (tpt)
REVERT: A  417 HIS cc_start: 0.9450 (t-170) cc_final: 0.9218 (t-170)
REVERT: A  441 LYS cc_start: 0.8657 (tmtt) cc_final: 0.8278 (tptt)
REVERT: A  455 MET cc_start: 0.8626 (ppp) cc_final: 0.7927 (ppp)
REVERT: A  461 TRP cc_start: 0.8635 (m-10) cc_final: 0.8297 (m-90)
REVERT: A  480 MET cc_start: 0.8856 (tpt) cc_final: 0.8433 (tpt)
REVERT: A  505 HIS cc_start: 0.8613 (m90) cc_final: 0.8349 (m90)
REVERT: A  516 TYR cc_start: 0.8659 (t80) cc_final: 0.8279 (t80)
REVERT: A  519 THR cc_start: 0.9655 (p) cc_final: 0.9399 (p)
REVERT: A  523 PHE cc_start: 0.9504 (m-80) cc_final: 0.8993 (m-80)
REVERT: A  525 PHE cc_start: 0.9509 (m-80) cc_final: 0.9202 (m-80)
REVERT: A  554 LEU cc_start: 0.9184 (tp) cc_final: 0.8907 (tp)
REVERT: A  564 GLU cc_start: 0.8986 (mp0) cc_final: 0.8560 (mp0)
REVERT: D  386 LYS cc_start: 0.8907 (pttp) cc_final: 0.8435 (pttm)
REVERT: D  444 LYS cc_start: 0.9559 (ttmt) cc_final: 0.9233 (ttmm)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.0726
  time to fit residues: 15.9323
Evaluate side-chains
  147 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 1 optimal weight:   10.0000
   chunk 42 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 56 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 6 optimal weight:    9.9990
   chunk 73 optimal weight:   10.0000
   overall best weight:    1.3582

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

Flipped N/Q/H residues before XYZ refinement:
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 241 HIS
A 535 HIS
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 599 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.091167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.072245 restraints weight = 26935.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.074627 restraints weight = 19045.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.076442 restraints weight = 14566.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.077860 restraints weight = 11740.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.078975 restraints weight = 9805.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.7215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6585  Z= 0.138
  Angle     :  0.668   6.663   8952  Z= 0.346
  Chirality :  0.045   0.181    931
  Planarity :  0.004   0.038   1159
  Dihedral  :  4.893  23.260    854
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 15.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.30), residues: 783
  helix:  0.33 (0.27), residues: 375
  sheet: -1.13 (0.73), residues: 44
  loop : -1.11 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 177 
 TYR   0.014   0.001   TYR A 516 
 PHE   0.028   0.001   PHE A 356 
 TRP   0.021   0.002   TRP A 302 
 HIS   0.010   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6578)
  covalent geometry    : angle       0.66742 ( 8938)
  SS BOND              : bond        0.00316 (    7)
  SS BOND              : angle       0.82159 (   14)
  hydrogen bonds       : bond        0.04079 (  272)
  hydrogen bonds       : angle       5.24724 (  795)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.9529 (ppp) cc_final: 0.9302 (ppp)
REVERT: A   82 MET cc_start: 0.8229 (ppp) cc_final: 0.7963 (ppp)
REVERT: A  154 ASN cc_start: 0.8872 (m-40) cc_final: 0.8567 (m110)
REVERT: A  176 LEU cc_start: 0.8197 (mm) cc_final: 0.7580 (mm)
REVERT: A  207 TYR cc_start: 0.9379 (m-80) cc_final: 0.8978 (m-80)
REVERT: A  215 TYR cc_start: 0.8788 (m-80) cc_final: 0.8407 (m-80)
REVERT: A  227 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8632 (mm-30)
REVERT: A  237 TYR cc_start: 0.8635 (t80) cc_final: 0.8220 (t80)
REVERT: A  270 MET cc_start: 0.8893 (tpp) cc_final: 0.8054 (tpp)
REVERT: A  315 PHE cc_start: 0.9509 (m-10) cc_final: 0.8258 (m-10)
REVERT: A  376 MET cc_start: 0.9389 (tpt) cc_final: 0.8723 (tpt)
REVERT: A  417 HIS cc_start: 0.9475 (t-170) cc_final: 0.9183 (t-170)
REVERT: A  441 LYS cc_start: 0.8675 (tmtt) cc_final: 0.8339 (tptt)
REVERT: A  455 MET cc_start: 0.8547 (ppp) cc_final: 0.7770 (ppp)
REVERT: A  461 TRP cc_start: 0.8699 (m-10) cc_final: 0.8397 (m-90)
REVERT: A  480 MET cc_start: 0.8845 (tpt) cc_final: 0.8425 (tpt)
REVERT: A  505 HIS cc_start: 0.8768 (m90) cc_final: 0.8413 (m90)
REVERT: A  512 PHE cc_start: 0.8235 (m-80) cc_final: 0.7958 (m-80)
REVERT: A  516 TYR cc_start: 0.8668 (t80) cc_final: 0.8300 (t80)
REVERT: A  519 THR cc_start: 0.9681 (p) cc_final: 0.9476 (p)
REVERT: A  523 PHE cc_start: 0.9517 (m-80) cc_final: 0.9032 (m-80)
REVERT: A  525 PHE cc_start: 0.9505 (m-80) cc_final: 0.9197 (m-80)
REVERT: A  554 LEU cc_start: 0.9230 (tp) cc_final: 0.9001 (tp)
REVERT: A  564 GLU cc_start: 0.8985 (mp0) cc_final: 0.8576 (mp0)
REVERT: D  444 LYS cc_start: 0.9529 (ttmt) cc_final: 0.9145 (ttmm)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.0728
  time to fit residues: 16.2575
Evaluate side-chains
  143 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 73 optimal weight:    6.9990
   chunk 54 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 70 optimal weight:   10.0000
   chunk 48 optimal weight:    0.6980
   chunk 76 optimal weight:    5.9990
   chunk 46 optimal weight:    8.9990
   chunk 42 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 57 optimal weight:    0.5980
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 HIS
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 599 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.091954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.073056 restraints weight = 28300.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.075295 restraints weight = 20509.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.077061 restraints weight = 15978.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.078462 restraints weight = 13019.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.079529 restraints weight = 10980.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.7381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6585  Z= 0.136
  Angle     :  0.686   8.258   8952  Z= 0.357
  Chirality :  0.045   0.188    931
  Planarity :  0.004   0.039   1159
  Dihedral  :  4.866  23.955    854
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 14.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.72 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.30), residues: 783
  helix:  0.28 (0.27), residues: 379
  sheet: -1.12 (0.72), residues: 44
  loop : -1.09 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 306 
 TYR   0.014   0.001   TYR D 495 
 PHE   0.027   0.001   PHE A 356 
 TRP   0.030   0.002   TRP A 473 
 HIS   0.008   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6578)
  covalent geometry    : angle       0.68469 ( 8938)
  SS BOND              : bond        0.00245 (    7)
  SS BOND              : angle       1.26077 (   14)
  hydrogen bonds       : bond        0.04127 (  272)
  hydrogen bonds       : angle       5.24606 (  795)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1282.06 seconds
wall clock time: 22 minutes 47.54 seconds (1367.54 seconds total)