Starting phenix.real_space_refine
on Tue Feb  3 17:36:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qsc_53335/02_2026/9qsc_53335.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qsc_53335/02_2026/9qsc_53335.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qsc_53335/02_2026/9qsc_53335.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qsc_53335/02_2026/9qsc_53335.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qsc_53335/02_2026/9qsc_53335.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qsc_53335/02_2026/9qsc_53335.map"
  }
  resolution = 3.2
  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=   0.001 sd=   0.024
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: 5
    Type Number    sf(0)   Gaussians
     P      19      5.49       5
     S      16      5.16       5
     C    3529      2.51       5
     N     949      2.21       5
     O    1088      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5601
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5194
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 626, 5194
          Classifications: {'peptide': 626}
          Link IDs: {'PTRANS': 9, 'TRANS': 616}
    Chain: "B"
      Number of atoms: 203
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 203
          Classifications: {'DNA': 10}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 9}
    Chain: "C"
      Number of atoms: 204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 204
          Classifications: {'DNA': 10}
          Link IDs: {'rna3p': 9}
  Time building chain proxies: 1.48, per 1000 atoms: 0.26
  Number of scatterers: 5601
  At special positions: 0
  Unit cell: (71.02, 89.04, 111.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      16     16.00
     P      19     15.00
     O    1088      8.00
     N     949      7.00
     C    3529      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 304.7 milliseconds
  

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1224

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 7 sheets defined
      55.9% alpha, 12.6% beta
      9 base pairs and 13 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 10
    Processing helix  chain 'A' and resid 66 through 74
      removed outlier: 3.807A  pdb=" N   ASN A  70 " --> pdb=" O   GLU A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 115
      No H-bonds generated for 'chain 'A' and resid 113 through 115'
    Processing helix  chain 'A' and resid 117 through 120
    Processing helix  chain 'A' and resid 121 through 130
      removed outlier: 3.506A  pdb=" N   LYS A 126 " --> pdb=" O   ASP A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 150
      removed outlier: 3.817A  pdb=" N   ASP A 143 " --> pdb=" O   ASN A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 169
    Processing helix  chain 'A' and resid 177 through 187
    Processing helix  chain 'A' and resid 206 through 234
      removed outlier: 4.639A  pdb=" N   LEU A 219 " --> pdb=" O   ASP A 215 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   LEU A 220 " --> pdb=" O   SER A 216 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   LYS A 221 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   GLU A 228 " --> pdb=" O   LYS A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 245
    Processing helix  chain 'A' and resid 245 through 256
    Processing helix  chain 'A' and resid 260 through 287
    Processing helix  chain 'A' and resid 295 through 307
    Processing helix  chain 'A' and resid 320 through 327
      removed outlier: 3.918A  pdb=" N   ASN A 326 " --> pdb=" O   SER A 322 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   PHE A 327 " --> pdb=" O   ASN A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 349
      removed outlier: 3.523A  pdb=" N   ILE A 334 " --> pdb=" O   HIS A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 356
    Processing helix  chain 'A' and resid 384 through 388
      removed outlier: 3.543A  pdb=" N   ILE A 388 " --> pdb=" O   LEU A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 396
    Processing helix  chain 'A' and resid 413 through 424
    Processing helix  chain 'A' and resid 425 through 434
      removed outlier: 3.522A  pdb=" N   LEU A 429 " --> pdb=" O   ASP A 425 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LYS A 430 " --> pdb=" O   GLU A 426 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ASN A 434 " --> pdb=" O   LYS A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 437 through 448
    Processing helix  chain 'A' and resid 450 through 454
    Processing helix  chain 'A' and resid 455 through 470
      removed outlier: 3.749A  pdb=" N   PHE A 467 " --> pdb=" O   LYS A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 487
      removed outlier: 4.137A  pdb=" N   LYS A 479 " --> pdb=" O   TYR A 475 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   ASN A 480 " --> pdb=" O   VAL A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 506
      removed outlier: 3.539A  pdb=" N   HIS A 505 " --> pdb=" O   SER A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 520
      removed outlier: 3.600A  pdb=" N   TYR A 510 " --> pdb=" O   TYR A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 566
      Proline residue:  A 546  - end of helix
      removed outlier: 3.625A  pdb=" N   ASP A 564 " --> pdb=" O   VAL A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 609
      removed outlier: 3.797A  pdb=" N   LEU A 594 " --> pdb=" O   GLN A 590 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LYS A 595 " --> pdb=" O   GLU A 591 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   PHE A 608 " --> pdb=" O   SER A 604 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13
    Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 29
      removed outlier: 3.619A  pdb=" N   ASP A  24 " --> pdb=" O   PHE A  40 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 57 through 60
      removed outlier: 6.329A  pdb=" N   LYS A 135 " --> pdb=" O   PHE A 158 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 363 through 364
      removed outlier: 3.726A  pdb=" N   LYS A 258 " --> pdb=" O   ILE A 399 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 367 through 369
      removed outlier: 3.888A  pdb=" N   THR A 367 " --> pdb=" O   GLU A 381 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 572 through 577
      removed outlier: 6.856A  pdb=" N   ILE A 582 " --> pdb=" O   ILE A 574 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   CYS A 576 " --> pdb=" O   GLU A 580 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   GLU A 580 " --> pdb=" O   CYS A 576 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 523 through 525

    269 hydrogen bonds defined for protein.
    759 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      21 hydrogen bonds
      42 hydrogen bond angles
      0 basepair planarities
      9 basepair parallelities
      13 stacking parallelities
  Total time for adding SS restraints: 0.94

  Time building geometry restraints manager: 0.66 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1652
        1.33 -     1.45: 840
        1.45 -     1.57: 3183
        1.57 -     1.69: 37
        1.69 -     1.81: 23
  Bond restraints: 5735
  Sorted by residual:
  bond pdb=" P    DA C  16 "
       pdb=" OP2  DA C  16 "
    ideal  model  delta    sigma   weight residual
    1.480  1.518 -0.038 2.00e-02 2.50e+03 3.61e+00
  bond pdb=" P    DA B  24 "
       pdb=" OP2  DA B  24 "
    ideal  model  delta    sigma   weight residual
    1.480  1.518 -0.038 2.00e-02 2.50e+03 3.58e+00
  bond pdb=" P    DC C  17 "
       pdb=" OP1  DC C  17 "
    ideal  model  delta    sigma   weight residual
    1.480  1.517 -0.037 2.00e-02 2.50e+03 3.43e+00
  bond pdb=" P    DA C  16 "
       pdb=" OP1  DA C  16 "
    ideal  model  delta    sigma   weight residual
    1.480  1.517 -0.037 2.00e-02 2.50e+03 3.40e+00
  bond pdb=" P    DC C  17 "
       pdb=" OP2  DC C  17 "
    ideal  model  delta    sigma   weight residual
    1.480  1.516 -0.036 2.00e-02 2.50e+03 3.24e+00
  ... (remaining 5730 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 7626
        1.41 -     2.83: 152
        2.83 -     4.24: 17
        4.24 -     5.66: 7
        5.66 -     7.07: 5
  Bond angle restraints: 7807
  Sorted by residual:
  angle pdb=" CA  LYS A 382 "
        pdb=" C   LYS A 382 "
        pdb=" N   PRO A 383 "
      ideal   model   delta    sigma   weight residual
     118.44  123.01   -4.57 1.59e+00 3.96e-01 8.28e+00
  angle pdb=" C   LYS A 382 "
        pdb=" CA  LYS A 382 "
        pdb=" CB  LYS A 382 "
      ideal   model   delta    sigma   weight residual
     110.17  115.74   -5.57 1.97e+00 2.58e-01 8.00e+00
  angle pdb=" O3'  DG B  23 "
        pdb=" P    DA B  24 "
        pdb=" O5'  DA B  24 "
      ideal   model   delta    sigma   weight residual
     104.00  107.95   -3.95 1.50e+00 4.44e-01 6.94e+00
  angle pdb=" C3'  DG B  23 "
        pdb=" C2'  DG B  23 "
        pdb=" C1'  DG B  23 "
      ideal   model   delta    sigma   weight residual
     101.60  105.32   -3.72 1.50e+00 4.44e-01 6.15e+00
  angle pdb=" OP1  DA B  24 "
        pdb=" P    DA B  24 "
        pdb=" OP2  DA B  24 "
      ideal   model   delta    sigma   weight residual
     120.00  112.93    7.07 3.00e+00 1.11e-01 5.55e+00
  ... (remaining 7802 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.91: 3132
       16.91 -    33.82: 229
       33.82 -    50.73: 71
       50.73 -    67.63: 31
       67.63 -    84.54: 2
  Dihedral angle restraints: 3465
    sinusoidal: 1585
      harmonic: 1880
  Sorted by residual:
  dihedral pdb=" CA  LYS A 382 "
           pdb=" C   LYS A 382 "
           pdb=" N   PRO A 383 "
           pdb=" CA  PRO A 383 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.98   22.02     0      5.00e+00 4.00e-02 1.94e+01
  dihedral pdb=" CA  LYS A 417 "
           pdb=" CB  LYS A 417 "
           pdb=" CG  LYS A 417 "
           pdb=" CD  LYS A 417 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.28  -58.72     3      1.50e+01 4.44e-03 9.47e+00
  dihedral pdb=" CB  LYS A 224 "
           pdb=" CG  LYS A 224 "
           pdb=" CD  LYS A 224 "
           pdb=" CE  LYS A 224 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -124.97  -55.03     3      1.50e+01 4.44e-03 9.32e+00
  ... (remaining 3462 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.128: 866
       0.128 -    0.256: 7
       0.256 -    0.383: 0
       0.383 -    0.511: 0
       0.511 -    0.639: 3
  Chirality restraints: 876
  Sorted by residual:
  chirality pdb=" P    DA B  24 "
            pdb=" OP1  DA B  24 "
            pdb=" OP2  DA B  24 "
            pdb=" O5'  DA B  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.98   -0.64 2.00e-01 2.50e+01 1.02e+01
  chirality pdb=" P    DC C  17 "
            pdb=" OP1  DC C  17 "
            pdb=" OP2  DC C  17 "
            pdb=" O5'  DC C  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.91   -0.56 2.00e-01 2.50e+01 7.98e+00
  chirality pdb=" P    DA C  16 "
            pdb=" OP1  DA C  16 "
            pdb=" OP2  DA C  16 "
            pdb=" O5'  DA C  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.89   -0.55 2.00e-01 2.50e+01 7.50e+00
  ... (remaining 873 not shown)

  Planarity restraints: 929
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 247 "   -0.029 5.00e-02 4.00e+02   4.37e-02 3.06e+00
        pdb=" N   PRO A 248 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 248 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 248 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 382 "    0.022 5.00e-02 4.00e+02   3.30e-02 1.74e+00
        pdb=" N   PRO A 383 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 383 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 383 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 353 "   -0.019 5.00e-02 4.00e+02   2.82e-02 1.28e+00
        pdb=" N   PRO A 354 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A 354 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 354 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 926 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 83
        2.67 -     3.22: 5391
        3.22 -     3.78: 8329
        3.78 -     4.34: 11551
        4.34 -     4.90: 18668
  Nonbonded interactions: 44022
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 296 "
            pdb=" OG1 THR A 319 "
     model   vdw
     2.106 3.040
  nonbonded pdb=" O   LYS A 305 "
            pdb=" ND2 ASN A 307 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" O   ASP A  16 "
            pdb=" ND2 ASN A  18 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" NZ  LYS A 283 "
            pdb=" O   ILE A 291 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" OD1 ASN A 205 "
            pdb=" NE2 GLN A 208 "
     model   vdw
     2.294 3.120
  ... (remaining 44017 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.720
  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:             0.020
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.370
  Find NCS groups from input model:        0.020
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
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      :  0.004   0.058   5735  Z= 0.180
  Angle     :  0.541   7.069   7807  Z= 0.299
  Chirality :  0.053   0.639    876
  Planarity :  0.003   0.044    929
  Dihedral  : 14.159  84.542   2241
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.24 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  2.89 %
    Favored  : 96.77 %
  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 (0.34), residues: 624
  helix:  1.18 (0.30), residues: 301
  sheet: -0.52 (0.64), residues: 64
  loop : -0.06 (0.41), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 459 
 TYR   0.011   0.001   TYR A 499 
 PHE   0.012   0.002   PHE A 406 
 TRP   0.004   0.001   TRP A 199 
 HIS   0.004   0.001   HIS A 236 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 5735)
  covalent geometry    : angle       0.54126 ( 7807)
  hydrogen bonds       : bond        0.16856 (  290)
  hydrogen bonds       : angle       7.15022 (  801)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 211
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 LYS cc_start: 0.8681 (mttt) cc_final: 0.8289 (mtmm)
REVERT: A   21 LYS cc_start: 0.8610 (tttp) cc_final: 0.8394 (tttt)
REVERT: A   29 LYS cc_start: 0.8551 (mmmt) cc_final: 0.8322 (mmmt)
REVERT: A   30 ASN cc_start: 0.8258 (t0) cc_final: 0.8025 (t0)
REVERT: A   35 ILE cc_start: 0.8855 (mt) cc_final: 0.7871 (mt)
REVERT: A   47 LYS cc_start: 0.8487 (tttt) cc_final: 0.8085 (tttt)
REVERT: A   55 SER cc_start: 0.8352 (p) cc_final: 0.8137 (m)
REVERT: A   64 ASN cc_start: 0.8149 (t0) cc_final: 0.7692 (t0)
REVERT: A   68 ASN cc_start: 0.8576 (m-40) cc_final: 0.8374 (m-40)
REVERT: A   89 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7519 (mm-30)
REVERT: A  117 LYS cc_start: 0.8099 (mttm) cc_final: 0.7805 (mttm)
REVERT: A  143 ASP cc_start: 0.7888 (m-30) cc_final: 0.7612 (m-30)
REVERT: A  177 LYS cc_start: 0.8135 (mttp) cc_final: 0.7874 (mttt)
REVERT: A  201 ASN cc_start: 0.8065 (t0) cc_final: 0.7847 (t0)
REVERT: A  203 LEU cc_start: 0.8159 (mt) cc_final: 0.7857 (mt)
REVERT: A  205 ASN cc_start: 0.7832 (p0) cc_final: 0.7625 (p0)
REVERT: A  206 ASN cc_start: 0.8063 (t0) cc_final: 0.7790 (t0)
REVERT: A  260 ASP cc_start: 0.7963 (t0) cc_final: 0.7519 (t0)
REVERT: A  280 ASP cc_start: 0.8053 (t0) cc_final: 0.7725 (t0)
REVERT: A  289 GLU cc_start: 0.7907 (pp20) cc_final: 0.7672 (pp20)
REVERT: A  319 THR cc_start: 0.7496 (p) cc_final: 0.6768 (p)
REVERT: A  412 LYS cc_start: 0.8676 (mtmt) cc_final: 0.8323 (mtmm)
REVERT: A  425 ASP cc_start: 0.7867 (t0) cc_final: 0.7578 (t0)
REVERT: A  428 MET cc_start: 0.8390 (mtt) cc_final: 0.8131 (mtt)
REVERT: A  430 LYS cc_start: 0.8441 (ttpp) cc_final: 0.8166 (ttmm)
REVERT: A  450 ASN cc_start: 0.7455 (t0) cc_final: 0.7203 (t0)
REVERT: A  455 ASN cc_start: 0.7955 (p0) cc_final: 0.7440 (p0)
REVERT: A  463 LYS cc_start: 0.8001 (tptm) cc_final: 0.7436 (tppp)
REVERT: A  494 GLN cc_start: 0.8261 (mt0) cc_final: 0.7588 (mt0)
REVERT: A  499 TYR cc_start: 0.8472 (t80) cc_final: 0.8222 (t80)
REVERT: A  517 LYS cc_start: 0.8586 (ttmt) cc_final: 0.8272 (ttmm)
REVERT: A  519 LYS cc_start: 0.8661 (tppp) cc_final: 0.8411 (tppt)
REVERT: A  524 TYR cc_start: 0.8063 (m-80) cc_final: 0.7713 (m-80)
REVERT: A  580 GLU cc_start: 0.8074 (tt0) cc_final: 0.7823 (tt0)
  outliers start: 2
  outliers final: 2
  residues processed: 212
  average time/residue: 0.0979
  time to fit residues: 25.2996
Evaluate side-chains
  195 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 193
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  374 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0270
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.7638

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN
A 170 ASN
A 297 GLN
A 386 GLN
A 480 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.142463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.119575 restraints weight = 7952.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 2.14
r_work: 0.3395 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5735  Z= 0.181
  Angle     :  0.547   7.007   7807  Z= 0.307
  Chirality :  0.046   0.140    876
  Planarity :  0.004   0.042    929
  Dihedral  : 15.841  59.470    887
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.76 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 10.19 %
    Favored  : 87.95 %
  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:  1.11 (0.35), residues: 624
  helix:  1.37 (0.30), residues: 302
  sheet: -0.47 (0.57), residues: 74
  loop :  0.51 (0.43), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 340 
 TYR   0.014   0.002   TYR A 475 
 PHE   0.018   0.002   PHE A 502 
 TRP   0.006   0.001   TRP A 512 
 HIS   0.004   0.001   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 5735)
  covalent geometry    : angle       0.54695 ( 7807)
  hydrogen bonds       : bond        0.04945 (  290)
  hydrogen bonds       : angle       4.91861 (  801)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 198
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A   17 ASP cc_start: 0.7984 (t0) cc_final: 0.7736 (t0)
REVERT: A   21 LYS cc_start: 0.8581 (tttp) cc_final: 0.8330 (tttp)
REVERT: A   34 GLU cc_start: 0.7423 (tp30) cc_final: 0.7150 (tp30)
REVERT: A   35 ILE cc_start: 0.8494 (mt) cc_final: 0.8079 (mt)
REVERT: A   36 THR cc_start: 0.8669 (t) cc_final: 0.8225 (p)
REVERT: A   37 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8051 (mm-30)
REVERT: A   60 ILE cc_start: 0.8357 (mm) cc_final: 0.8098 (mt)
REVERT: A   89 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7657 (mm-30)
REVERT: A  117 LYS cc_start: 0.8114 (mttm) cc_final: 0.7742 (mttm)
REVERT: A  201 ASN cc_start: 0.8043 (t0) cc_final: 0.7726 (t0)
REVERT: A  203 LEU cc_start: 0.8325 (mt) cc_final: 0.8087 (mp)
REVERT: A  205 ASN cc_start: 0.7974 (p0) cc_final: 0.7735 (p0)
REVERT: A  206 ASN cc_start: 0.7793 (t0) cc_final: 0.7560 (t0)
REVERT: A  233 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7530 (mm-30)
REVERT: A  260 ASP cc_start: 0.7823 (t0) cc_final: 0.7464 (t0)
REVERT: A  280 ASP cc_start: 0.8154 (t0) cc_final: 0.7778 (t0)
REVERT: A  292 ASN cc_start: 0.7913 (t0) cc_final: 0.7225 (t0)
REVERT: A  319 THR cc_start: 0.7718 (p) cc_final: 0.7379 (p)
REVERT: A  380 SER cc_start: 0.8263 (p) cc_final: 0.7981 (p)
REVERT: A  410 ASP cc_start: 0.7397 (p0) cc_final: 0.7131 (p0)
REVERT: A  412 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8354 (mtmm)
REVERT: A  425 ASP cc_start: 0.7657 (t0) cc_final: 0.7405 (t0)
REVERT: A  430 LYS cc_start: 0.8470 (ttpp) cc_final: 0.8203 (ttmm)
REVERT: A  447 THR cc_start: 0.8746 (p) cc_final: 0.8341 (t)
REVERT: A  463 LYS cc_start: 0.8015 (tptm) cc_final: 0.7486 (tppp)
REVERT: A  499 TYR cc_start: 0.8328 (t80) cc_final: 0.8127 (t80)
REVERT: A  517 LYS cc_start: 0.8512 (ttmt) cc_final: 0.8193 (ttmm)
REVERT: A  580 GLU cc_start: 0.8200 (tt0) cc_final: 0.7991 (tt0)
REVERT: A  584 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7274 (mt-10)
  outliers start: 11
  outliers final: 6
  residues processed: 202
  average time/residue: 0.0928
  time to fit residues: 23.1566
Evaluate side-chains
  198 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 192
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  604 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 39 optimal weight:    0.0980
   chunk 15 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0870
   chunk 41 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
A  64 ASN
A  68 ASN
A 413 GLN
A 477 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.143283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.120158 restraints weight = 7930.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 2.12
r_work: 0.3403 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5735  Z= 0.141
  Angle     :  0.518   6.570   7807  Z= 0.290
  Chirality :  0.043   0.141    876
  Planarity :  0.003   0.047    929
  Dihedral  : 15.811  59.974    885
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.12 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 13.24 %
    Favored  : 84.21 %
  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:  1.10 (0.34), residues: 624
  helix:  1.46 (0.30), residues: 302
  sheet: -0.28 (0.60), residues: 76
  loop :  0.30 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 340 
 TYR   0.024   0.001   TYR A 475 
 PHE   0.015   0.002   PHE A 502 
 TRP   0.006   0.001   TRP A 512 
 HIS   0.007   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 5735)
  covalent geometry    : angle       0.51833 ( 7807)
  hydrogen bonds       : bond        0.04245 (  290)
  hydrogen bonds       : angle       4.67717 (  801)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 197
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8640 (mmmt) cc_final: 0.8334 (tppt)
REVERT: A   21 LYS cc_start: 0.8713 (tttp) cc_final: 0.8499 (tttp)
REVERT: A   29 LYS cc_start: 0.8374 (mmmt) cc_final: 0.8006 (mmmm)
REVERT: A   37 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8184 (mm-30)
REVERT: A   60 ILE cc_start: 0.8388 (mm) cc_final: 0.8154 (mt)
REVERT: A   89 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7928 (mm-30)
REVERT: A   93 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7600 (mm-30)
REVERT: A   97 LEU cc_start: 0.8330 (mt) cc_final: 0.8088 (mt)
REVERT: A  117 LYS cc_start: 0.8299 (mttm) cc_final: 0.7949 (mttm)
REVERT: A  168 ASP cc_start: 0.8271 (m-30) cc_final: 0.7994 (t0)
REVERT: A  201 ASN cc_start: 0.8136 (t0) cc_final: 0.7843 (t0)
REVERT: A  203 LEU cc_start: 0.8374 (mt) cc_final: 0.8117 (mp)
REVERT: A  205 ASN cc_start: 0.8239 (p0) cc_final: 0.8026 (p0)
REVERT: A  233 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7718 (mm-30)
REVERT: A  260 ASP cc_start: 0.7946 (t0) cc_final: 0.7506 (t0)
REVERT: A  280 ASP cc_start: 0.8337 (t0) cc_final: 0.7937 (t0)
REVERT: A  292 ASN cc_start: 0.7954 (t0) cc_final: 0.7568 (t0)
REVERT: A  319 THR cc_start: 0.7735 (p) cc_final: 0.7371 (p)
REVERT: A  380 SER cc_start: 0.8256 (p) cc_final: 0.7945 (p)
REVERT: A  410 ASP cc_start: 0.7634 (p0) cc_final: 0.7367 (p0)
REVERT: A  412 LYS cc_start: 0.8776 (mtmt) cc_final: 0.8458 (mtmm)
REVERT: A  425 ASP cc_start: 0.7871 (t0) cc_final: 0.7651 (t0)
REVERT: A  430 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8338 (ttmm)
REVERT: A  447 THR cc_start: 0.8832 (p) cc_final: 0.8433 (t)
REVERT: A  463 LYS cc_start: 0.8157 (tptm) cc_final: 0.7633 (tppp)
REVERT: A  474 ASN cc_start: 0.8409 (t0) cc_final: 0.8064 (t0)
REVERT: A  499 TYR cc_start: 0.8464 (t80) cc_final: 0.8213 (t80)
REVERT: A  517 LYS cc_start: 0.8480 (ttmt) cc_final: 0.8131 (ttmm)
REVERT: A  580 GLU cc_start: 0.8275 (tt0) cc_final: 0.8064 (tt0)
REVERT: A  584 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7607 (mt-10)
REVERT: A  623 ASN cc_start: 0.8270 (p0) cc_final: 0.7943 (p0)
  outliers start: 15
  outliers final: 7
  residues processed: 201
  average time/residue: 0.0785
  time to fit residues: 19.7495
Evaluate side-chains
  198 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 191
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  564 ASP
Chi-restraints excluded: chain A residue  604 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 50 optimal weight:    0.0870
   chunk 16 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 34 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A 170 ASN
A 208 GLN
A 297 GLN
A 318 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.142545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.119533 restraints weight = 7904.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 2.13
r_work: 0.3388 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.2447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5735  Z= 0.156
  Angle     :  0.510   6.271   7807  Z= 0.285
  Chirality :  0.044   0.151    876
  Planarity :  0.003   0.050    929
  Dihedral  : 15.792  59.771    885
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.76 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 14.77 %
    Favored  : 82.00 %
  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:  1.07 (0.34), residues: 624
  helix:  1.50 (0.30), residues: 302
  sheet: -0.46 (0.54), residues: 87
  loop :  0.31 (0.43), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 340 
 TYR   0.023   0.001   TYR A  65 
 PHE   0.016   0.002   PHE A  58 
 TRP   0.005   0.001   TRP A 512 
 HIS   0.003   0.001   HIS A 513 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 5735)
  covalent geometry    : angle       0.51033 ( 7807)
  hydrogen bonds       : bond        0.04134 (  290)
  hydrogen bonds       : angle       4.55511 (  801)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 199
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8559 (mmmt) cc_final: 0.8246 (tppt)
REVERT: A   29 LYS cc_start: 0.8201 (mmmt) cc_final: 0.7879 (mmmm)
REVERT: A   34 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7339 (mp0)
REVERT: A   37 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7908 (mm-30)
REVERT: A   60 ILE cc_start: 0.8415 (mm) cc_final: 0.8177 (mt)
REVERT: A   68 ASN cc_start: 0.8460 (m-40) cc_final: 0.8204 (m110)
REVERT: A   89 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7596 (mm-30)
REVERT: A   93 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7440 (mm-30)
REVERT: A  103 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7236 (tm-30)
REVERT: A  117 LYS cc_start: 0.8236 (mttm) cc_final: 0.7868 (mttm)
REVERT: A  168 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7730 (t0)
REVERT: A  201 ASN cc_start: 0.7994 (t0) cc_final: 0.7728 (t0)
REVERT: A  203 LEU cc_start: 0.8423 (mt) cc_final: 0.8126 (mp)
REVERT: A  233 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7464 (mm-30)
REVERT: A  260 ASP cc_start: 0.7851 (t0) cc_final: 0.7422 (t0)
REVERT: A  285 LYS cc_start: 0.7876 (mttm) cc_final: 0.7555 (mttm)
REVERT: A  292 ASN cc_start: 0.7806 (t0) cc_final: 0.7454 (t0)
REVERT: A  293 VAL cc_start: 0.8443 (t) cc_final: 0.8191 (p)
REVERT: A  319 THR cc_start: 0.7741 (p) cc_final: 0.7199 (p)
REVERT: A  323 ASN cc_start: 0.7726 (t0) cc_final: 0.7282 (t0)
REVERT: A  340 ARG cc_start: 0.8550 (tpp80) cc_final: 0.8203 (tpp80)
REVERT: A  352 LYS cc_start: 0.8123 (mmmm) cc_final: 0.7847 (mmmm)
REVERT: A  380 SER cc_start: 0.8173 (p) cc_final: 0.7821 (p)
REVERT: A  410 ASP cc_start: 0.7410 (p0) cc_final: 0.7164 (p0)
REVERT: A  412 LYS cc_start: 0.8686 (mtmt) cc_final: 0.8320 (mtmm)
REVERT: A  425 ASP cc_start: 0.7647 (t0) cc_final: 0.7396 (t0)
REVERT: A  430 LYS cc_start: 0.8492 (ttpp) cc_final: 0.8278 (ttmm)
REVERT: A  436 ILE cc_start: 0.8825 (mt) cc_final: 0.8443 (tt)
REVERT: A  447 THR cc_start: 0.8722 (p) cc_final: 0.8319 (t)
REVERT: A  463 LYS cc_start: 0.8060 (tptm) cc_final: 0.7539 (tppp)
REVERT: A  474 ASN cc_start: 0.8238 (t0) cc_final: 0.7774 (t0)
REVERT: A  499 TYR cc_start: 0.8273 (t80) cc_final: 0.8063 (t80)
REVERT: A  517 LYS cc_start: 0.8410 (ttmt) cc_final: 0.8061 (ttmm)
REVERT: A  580 GLU cc_start: 0.8204 (tt0) cc_final: 0.7923 (tt0)
REVERT: A  584 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7263 (mt-10)
REVERT: A  623 ASN cc_start: 0.8018 (p0) cc_final: 0.7681 (p0)
  outliers start: 19
  outliers final: 12
  residues processed: 203
  average time/residue: 0.0801
  time to fit residues: 20.1545
Evaluate side-chains
  208 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 194
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   24 ASP
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain A residue   64 ASN
Chi-restraints excluded: chain A residue  168 ASP
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  172 ASN
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  564 ASP
Chi-restraints excluded: chain A residue  604 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 62 optimal weight:    6.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN
A 297 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.141465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.118570 restraints weight = 7983.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 2.15
r_work: 0.3370 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   5735  Z= 0.196
  Angle     :  0.527   6.023   7807  Z= 0.295
  Chirality :  0.045   0.150    876
  Planarity :  0.004   0.053    929
  Dihedral  : 15.769  59.699    885
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.92 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 16.64 %
    Favored  : 80.31 %
  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:  1.15 (0.35), residues: 624
  helix:  1.47 (0.30), residues: 301
  sheet: -0.26 (0.59), residues: 78
  loop :  0.39 (0.42), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 341 
 TYR   0.010   0.001   TYR A 223 
 PHE   0.017   0.002   PHE A  58 
 TRP   0.004   0.001   TRP A 512 
 HIS   0.003   0.001   HIS A 513 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 5735)
  covalent geometry    : angle       0.52724 ( 7807)
  hydrogen bonds       : bond        0.04322 (  290)
  hydrogen bonds       : angle       4.55672 (  801)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 203
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8571 (mmmt) cc_final: 0.8244 (tppt)
REVERT: A   29 LYS cc_start: 0.8251 (mmmt) cc_final: 0.7958 (mmmm)
REVERT: A   34 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7307 (pm20)
REVERT: A   60 ILE cc_start: 0.8426 (mm) cc_final: 0.8218 (mt)
REVERT: A   66 ASN cc_start: 0.8496 (t0) cc_final: 0.8228 (t0)
REVERT: A   68 ASN cc_start: 0.8465 (m-40) cc_final: 0.8211 (m110)
REVERT: A   89 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7598 (mm-30)
REVERT: A   93 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7398 (mm-30)
REVERT: A  103 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7249 (tm-30)
REVERT: A  117 LYS cc_start: 0.8242 (mttm) cc_final: 0.7790 (mttm)
REVERT: A  168 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7756 (t0)
REVERT: A  201 ASN cc_start: 0.7989 (t0) cc_final: 0.7724 (t0)
REVERT: A  203 LEU cc_start: 0.8345 (mt) cc_final: 0.8085 (mp)
REVERT: A  233 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7482 (mm-30)
REVERT: A  260 ASP cc_start: 0.7872 (t0) cc_final: 0.7429 (t0)
REVERT: A  280 ASP cc_start: 0.8103 (t0) cc_final: 0.7672 (t0)
REVERT: A  285 LYS cc_start: 0.7846 (mttm) cc_final: 0.7546 (mttm)
REVERT: A  292 ASN cc_start: 0.7905 (t0) cc_final: 0.7597 (t0)
REVERT: A  293 VAL cc_start: 0.8514 (t) cc_final: 0.8253 (p)
REVERT: A  319 THR cc_start: 0.7846 (p) cc_final: 0.7540 (p)
REVERT: A  323 ASN cc_start: 0.7703 (t0) cc_final: 0.7283 (t0)
REVERT: A  340 ARG cc_start: 0.8563 (tpp80) cc_final: 0.8267 (tpp80)
REVERT: A  352 LYS cc_start: 0.8121 (mmmm) cc_final: 0.7880 (mmmm)
REVERT: A  380 SER cc_start: 0.8162 (p) cc_final: 0.7758 (p)
REVERT: A  410 ASP cc_start: 0.7460 (p0) cc_final: 0.7205 (p0)
REVERT: A  412 LYS cc_start: 0.8721 (mtmt) cc_final: 0.8347 (mtmm)
REVERT: A  425 ASP cc_start: 0.7672 (t0) cc_final: 0.7402 (t0)
REVERT: A  436 ILE cc_start: 0.8812 (mt) cc_final: 0.8450 (tt)
REVERT: A  447 THR cc_start: 0.8701 (p) cc_final: 0.8323 (t)
REVERT: A  463 LYS cc_start: 0.8110 (tptm) cc_final: 0.7623 (tppp)
REVERT: A  499 TYR cc_start: 0.8323 (t80) cc_final: 0.8074 (t80)
REVERT: A  572 LYS cc_start: 0.8370 (mttp) cc_final: 0.7979 (mtpp)
REVERT: A  580 GLU cc_start: 0.8201 (tt0) cc_final: 0.7970 (tt0)
REVERT: A  584 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7248 (mt-10)
  outliers start: 18
  outliers final: 10
  residues processed: 208
  average time/residue: 0.0858
  time to fit residues: 22.0406
Evaluate side-chains
  211 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 199
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain A residue  168 ASP
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  483 ASN
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  505 HIS
Chi-restraints excluded: chain A residue  564 ASP
Chi-restraints excluded: chain A residue  604 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0670
   chunk 45 optimal weight:    0.0060
   chunk 39 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.3734

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

Flipped N/Q/H residues before XYZ refinement:
A 170 ASN
A 265 GLN
A 297 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.143494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.120471 restraints weight = 7950.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 2.15
r_work: 0.3404 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.2791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5735  Z= 0.124
  Angle     :  0.493   5.666   7807  Z= 0.275
  Chirality :  0.043   0.147    876
  Planarity :  0.003   0.055    929
  Dihedral  : 15.727  59.559    885
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.76 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 16.47 %
    Favored  : 80.31 %
  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:  1.31 (0.35), residues: 624
  helix:  1.63 (0.30), residues: 302
  sheet: -0.26 (0.60), residues: 78
  loop :  0.45 (0.43), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 395 
 TYR   0.007   0.001   TYR A 499 
 PHE   0.011   0.001   PHE A 502 
 TRP   0.007   0.002   TRP A 624 
 HIS   0.002   0.001   HIS A 513 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 5735)
  covalent geometry    : angle       0.49314 ( 7807)
  hydrogen bonds       : bond        0.03709 (  290)
  hydrogen bonds       : angle       4.45639 (  801)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 204
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8252 (tppt)
REVERT: A   21 LYS cc_start: 0.8695 (tttt) cc_final: 0.8474 (tttp)
REVERT: A   29 LYS cc_start: 0.8230 (mmmt) cc_final: 0.7932 (mmmm)
REVERT: A   41 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7487 (mt-10)
REVERT: A   58 PHE cc_start: 0.7650 (m-80) cc_final: 0.7197 (m-80)
REVERT: A   60 ILE cc_start: 0.8427 (mm) cc_final: 0.8204 (mt)
REVERT: A   68 ASN cc_start: 0.8425 (m-40) cc_final: 0.8193 (m110)
REVERT: A   89 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7566 (mm-30)
REVERT: A   93 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7366 (mm-30)
REVERT: A  103 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7305 (tm-30)
REVERT: A  117 LYS cc_start: 0.8219 (mttm) cc_final: 0.7795 (mttm)
REVERT: A  168 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7763 (t0)
REVERT: A  201 ASN cc_start: 0.7969 (t0) cc_final: 0.7720 (t0)
REVERT: A  203 LEU cc_start: 0.8321 (mt) cc_final: 0.8063 (mp)
REVERT: A  233 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7454 (mm-30)
REVERT: A  260 ASP cc_start: 0.7866 (t0) cc_final: 0.7428 (t0)
REVERT: A  285 LYS cc_start: 0.7686 (mttm) cc_final: 0.7256 (mttm)
REVERT: A  292 ASN cc_start: 0.7858 (t0) cc_final: 0.7610 (t0)
REVERT: A  319 THR cc_start: 0.7915 (p) cc_final: 0.7581 (p)
REVERT: A  323 ASN cc_start: 0.7687 (t0) cc_final: 0.7080 (t0)
REVERT: A  340 ARG cc_start: 0.8567 (tpp80) cc_final: 0.8128 (tpp80)
REVERT: A  352 LYS cc_start: 0.8109 (mmmm) cc_final: 0.7887 (mmmm)
REVERT: A  380 SER cc_start: 0.8080 (p) cc_final: 0.7620 (p)
REVERT: A  410 ASP cc_start: 0.7348 (p0) cc_final: 0.7052 (p0)
REVERT: A  412 LYS cc_start: 0.8678 (mtmt) cc_final: 0.8302 (mtmm)
REVERT: A  425 ASP cc_start: 0.7651 (t0) cc_final: 0.7375 (t0)
REVERT: A  436 ILE cc_start: 0.8772 (mt) cc_final: 0.8401 (tt)
REVERT: A  447 THR cc_start: 0.8716 (p) cc_final: 0.8308 (t)
REVERT: A  463 LYS cc_start: 0.8020 (tptm) cc_final: 0.7534 (tppp)
REVERT: A  469 LEU cc_start: 0.7445 (mt) cc_final: 0.7189 (mt)
REVERT: A  572 LYS cc_start: 0.8351 (mttp) cc_final: 0.7966 (mtpp)
REVERT: A  584 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7226 (mt-10)
  outliers start: 19
  outliers final: 13
  residues processed: 209
  average time/residue: 0.0790
  time to fit residues: 20.4352
Evaluate side-chains
  211 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 197
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   24 ASP
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  168 ASP
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  483 ASN
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  564 ASP
Chi-restraints excluded: chain A residue  604 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 11 optimal weight:    0.1980
   chunk 7 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 139 ASN
A 170 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.141930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.119086 restraints weight = 8140.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 2.12
r_work: 0.3387 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.2875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5735  Z= 0.167
  Angle     :  0.513   5.519   7807  Z= 0.288
  Chirality :  0.044   0.150    876
  Planarity :  0.003   0.058    929
  Dihedral  : 15.689  59.741    885
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.92 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 17.66 %
    Favored  : 79.29 %
  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:  1.23 (0.35), residues: 624
  helix:  1.55 (0.30), residues: 302
  sheet: -0.19 (0.60), residues: 78
  loop :  0.38 (0.43), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 395 
 TYR   0.010   0.001   TYR A 223 
 PHE   0.015   0.002   PHE A 502 
 TRP   0.004   0.001   TRP A 199 
 HIS   0.002   0.001   HIS A 513 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 5735)
  covalent geometry    : angle       0.51311 ( 7807)
  hydrogen bonds       : bond        0.03985 (  290)
  hydrogen bonds       : angle       4.41576 (  801)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 203
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8245 (tppt)
REVERT: A   18 ASN cc_start: 0.7640 (t0) cc_final: 0.7059 (t0)
REVERT: A   29 LYS cc_start: 0.8243 (mmmt) cc_final: 0.7960 (mmmm)
REVERT: A   34 GLU cc_start: 0.7643 (pm20) cc_final: 0.7352 (pm20)
REVERT: A   68 ASN cc_start: 0.8393 (m-40) cc_final: 0.8188 (m110)
REVERT: A   89 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7577 (mm-30)
REVERT: A   93 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7375 (mm-30)
REVERT: A  103 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7378 (tm-30)
REVERT: A  117 LYS cc_start: 0.8212 (mttm) cc_final: 0.7794 (mttm)
REVERT: A  168 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7736 (t0)
REVERT: A  201 ASN cc_start: 0.7985 (t0) cc_final: 0.7740 (t0)
REVERT: A  203 LEU cc_start: 0.8343 (mt) cc_final: 0.8056 (mp)
REVERT: A  233 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7425 (mm-30)
REVERT: A  260 ASP cc_start: 0.7910 (t0) cc_final: 0.7434 (t0)
REVERT: A  289 GLU cc_start: 0.7885 (pp20) cc_final: 0.7649 (pp20)
REVERT: A  293 VAL cc_start: 0.8438 (t) cc_final: 0.8195 (p)
REVERT: A  319 THR cc_start: 0.8001 (p) cc_final: 0.7627 (p)
REVERT: A  323 ASN cc_start: 0.7678 (t0) cc_final: 0.7277 (t0)
REVERT: A  410 ASP cc_start: 0.7434 (p0) cc_final: 0.7159 (p0)
REVERT: A  412 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8323 (mtmm)
REVERT: A  436 ILE cc_start: 0.8798 (mt) cc_final: 0.8441 (tt)
REVERT: A  447 THR cc_start: 0.8710 (p) cc_final: 0.8307 (t)
REVERT: A  463 LYS cc_start: 0.8047 (tptm) cc_final: 0.7694 (ttmm)
REVERT: A  469 LEU cc_start: 0.7435 (mt) cc_final: 0.7183 (mt)
REVERT: A  572 LYS cc_start: 0.8411 (mttp) cc_final: 0.8040 (mtpp)
REVERT: A  584 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7229 (mt-10)
  outliers start: 18
  outliers final: 12
  residues processed: 209
  average time/residue: 0.0883
  time to fit residues: 22.7765
Evaluate side-chains
  204 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 191
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   24 ASP
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  168 ASP
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  505 HIS
Chi-restraints excluded: chain A residue  564 ASP
Chi-restraints excluded: chain A residue  604 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 57 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 170 ASN
A 265 GLN
A 297 GLN
A 413 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.142309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.119507 restraints weight = 7979.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 2.09
r_work: 0.3390 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.2968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5735  Z= 0.163
  Angle     :  0.542   6.944   7807  Z= 0.296
  Chirality :  0.044   0.145    876
  Planarity :  0.003   0.062    929
  Dihedral  : 15.774  60.325    885
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.76 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 18.68 %
    Favored  : 77.93 %
  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:  1.29 (0.35), residues: 624
  helix:  1.60 (0.30), residues: 302
  sheet: -0.14 (0.61), residues: 78
  loop :  0.42 (0.43), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 395 
 TYR   0.010   0.001   TYR A  42 
 PHE   0.015   0.002   PHE A 502 
 TRP   0.005   0.001   TRP A 199 
 HIS   0.002   0.001   HIS A 513 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 5735)
  covalent geometry    : angle       0.54208 ( 7807)
  hydrogen bonds       : bond        0.03935 (  290)
  hydrogen bonds       : angle       4.40860 (  801)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 201
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8557 (mmmt) cc_final: 0.8244 (tppt)
REVERT: A   18 ASN cc_start: 0.7640 (t0) cc_final: 0.7034 (t0)
REVERT: A   29 LYS cc_start: 0.8257 (mmmt) cc_final: 0.7986 (mmmm)
REVERT: A   58 PHE cc_start: 0.7758 (m-80) cc_final: 0.7204 (m-80)
REVERT: A   64 ASN cc_start: 0.8004 (t0) cc_final: 0.7601 (t0)
REVERT: A   96 ARG cc_start: 0.7905 (tpt170) cc_final: 0.7693 (tpt-90)
REVERT: A  103 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7375 (tm-30)
REVERT: A  117 LYS cc_start: 0.8212 (mttm) cc_final: 0.7784 (mttm)
REVERT: A  168 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7777 (t0)
REVERT: A  177 LYS cc_start: 0.8281 (mttt) cc_final: 0.7980 (mmtp)
REVERT: A  201 ASN cc_start: 0.7988 (t0) cc_final: 0.7719 (t0)
REVERT: A  203 LEU cc_start: 0.8355 (mt) cc_final: 0.8033 (mp)
REVERT: A  233 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7409 (mm-30)
REVERT: A  260 ASP cc_start: 0.7903 (t0) cc_final: 0.7410 (t0)
REVERT: A  289 GLU cc_start: 0.7864 (pp20) cc_final: 0.7579 (pp20)
REVERT: A  296 GLN cc_start: 0.7451 (tp-100) cc_final: 0.6949 (tp-100)
REVERT: A  319 THR cc_start: 0.7921 (p) cc_final: 0.7425 (p)
REVERT: A  323 ASN cc_start: 0.7701 (t0) cc_final: 0.7296 (t0)
REVERT: A  340 ARG cc_start: 0.8502 (tpp80) cc_final: 0.8156 (tpp80)
REVERT: A  408 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8025 (mt)
REVERT: A  410 ASP cc_start: 0.7444 (p0) cc_final: 0.7184 (p0)
REVERT: A  412 LYS cc_start: 0.8720 (mtmt) cc_final: 0.8359 (mtmm)
REVERT: A  436 ILE cc_start: 0.8812 (mt) cc_final: 0.8475 (tt)
REVERT: A  447 THR cc_start: 0.8688 (p) cc_final: 0.8293 (t)
REVERT: A  463 LYS cc_start: 0.8024 (tptm) cc_final: 0.7607 (tppp)
REVERT: A  469 LEU cc_start: 0.7423 (mt) cc_final: 0.7188 (mt)
REVERT: A  572 LYS cc_start: 0.8402 (mttp) cc_final: 0.8029 (mtpp)
REVERT: A  580 GLU cc_start: 0.8298 (tt0) cc_final: 0.8093 (tt0)
REVERT: A  584 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7234 (mt-10)
  outliers start: 20
  outliers final: 16
  residues processed: 207
  average time/residue: 0.0977
  time to fit residues: 24.7814
Evaluate side-chains
  218 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 200
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   24 ASP
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  168 ASP
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  172 ASN
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  473 MET
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  505 HIS
Chi-restraints excluded: chain A residue  564 ASP
Chi-restraints excluded: chain A residue  604 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 11 optimal weight:    0.3980
   chunk 21 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 28 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0770
   overall best weight:    0.5940

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

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN
A 139 ASN
A 170 ASN
A 265 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.142514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.119946 restraints weight = 7998.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 2.10
r_work: 0.3394 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.3052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5735  Z= 0.157
  Angle     :  0.563   7.617   7807  Z= 0.309
  Chirality :  0.044   0.145    876
  Planarity :  0.003   0.061    929
  Dihedral  : 15.730  61.741    885
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.92 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 19.02 %
    Favored  : 77.76 %
  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:  1.24 (0.35), residues: 624
  helix:  1.60 (0.30), residues: 302
  sheet: -0.13 (0.61), residues: 78
  loop :  0.31 (0.43), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 395 
 TYR   0.010   0.001   TYR A  42 
 PHE   0.015   0.002   PHE A 502 
 TRP   0.005   0.001   TRP A 199 
 HIS   0.002   0.001   HIS A 513 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 5735)
  covalent geometry    : angle       0.56343 ( 7807)
  hydrogen bonds       : bond        0.03850 (  290)
  hydrogen bonds       : angle       4.39115 (  801)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 199
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8535 (mmmt) cc_final: 0.8238 (tppt)
REVERT: A   18 ASN cc_start: 0.7639 (t0) cc_final: 0.7027 (t0)
REVERT: A   29 LYS cc_start: 0.8204 (mmmt) cc_final: 0.7959 (mmmm)
REVERT: A   58 PHE cc_start: 0.7742 (m-80) cc_final: 0.7263 (m-80)
REVERT: A   64 ASN cc_start: 0.7994 (t0) cc_final: 0.7664 (t0)
REVERT: A   89 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7610 (mm-30)
REVERT: A   96 ARG cc_start: 0.7914 (tpt170) cc_final: 0.7674 (tpt-90)
REVERT: A  103 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7367 (tm-30)
REVERT: A  117 LYS cc_start: 0.8199 (mttm) cc_final: 0.7757 (mttm)
REVERT: A  168 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7742 (t0)
REVERT: A  177 LYS cc_start: 0.8289 (mttt) cc_final: 0.7989 (mmtp)
REVERT: A  201 ASN cc_start: 0.7992 (t0) cc_final: 0.7723 (t0)
REVERT: A  203 LEU cc_start: 0.8356 (mt) cc_final: 0.8012 (mp)
REVERT: A  233 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7456 (mm-30)
REVERT: A  260 ASP cc_start: 0.7912 (t0) cc_final: 0.7417 (t0)
REVERT: A  289 GLU cc_start: 0.7843 (pp20) cc_final: 0.7550 (pp20)
REVERT: A  296 GLN cc_start: 0.7449 (tp-100) cc_final: 0.7110 (tp-100)
REVERT: A  319 THR cc_start: 0.8001 (p) cc_final: 0.7376 (p)
REVERT: A  323 ASN cc_start: 0.7669 (t0) cc_final: 0.7063 (t0)
REVERT: A  340 ARG cc_start: 0.8580 (tpp80) cc_final: 0.8205 (tpp80)
REVERT: A  408 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8023 (mt)
REVERT: A  410 ASP cc_start: 0.7434 (p0) cc_final: 0.7178 (p0)
REVERT: A  412 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8344 (mtmm)
REVERT: A  436 ILE cc_start: 0.8802 (mt) cc_final: 0.8465 (tt)
REVERT: A  447 THR cc_start: 0.8695 (p) cc_final: 0.8305 (t)
REVERT: A  463 LYS cc_start: 0.8035 (tptm) cc_final: 0.7611 (tppp)
REVERT: A  469 LEU cc_start: 0.7422 (mt) cc_final: 0.7184 (mt)
REVERT: A  572 LYS cc_start: 0.8429 (mttp) cc_final: 0.8053 (mtpp)
REVERT: A  584 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7241 (mt-10)
  outliers start: 19
  outliers final: 14
  residues processed: 206
  average time/residue: 0.0887
  time to fit residues: 22.5384
Evaluate side-chains
  215 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 199
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   24 ASP
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  168 ASP
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  473 MET
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  505 HIS
Chi-restraints excluded: chain A residue  564 ASP
Chi-restraints excluded: chain A residue  604 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 17 optimal weight:    0.2980
   chunk 19 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 24 optimal weight:    0.3980
   chunk 47 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 297 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.141973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.119407 restraints weight = 8098.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 2.10
r_work: 0.3391 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.3116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5735  Z= 0.166
  Angle     :  0.572   7.193   7807  Z= 0.312
  Chirality :  0.044   0.146    876
  Planarity :  0.003   0.063    929
  Dihedral  : 15.661  64.096    885
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.92 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 19.69 %
    Favored  : 77.42 %
  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:  1.24 (0.35), residues: 624
  helix:  1.60 (0.30), residues: 302
  sheet: -0.20 (0.60), residues: 80
  loop :  0.35 (0.43), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 395 
 TYR   0.014   0.001   TYR A 339 
 PHE   0.015   0.002   PHE A 502 
 TRP   0.005   0.001   TRP A 199 
 HIS   0.002   0.001   HIS A 513 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 5735)
  covalent geometry    : angle       0.57172 ( 7807)
  hydrogen bonds       : bond        0.03893 (  290)
  hydrogen bonds       : angle       4.39790 (  801)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 199
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8261 (tppt)
REVERT: A   18 ASN cc_start: 0.7640 (t0) cc_final: 0.7016 (t0)
REVERT: A   29 LYS cc_start: 0.8231 (mmmt) cc_final: 0.7982 (mmmm)
REVERT: A   58 PHE cc_start: 0.7755 (m-80) cc_final: 0.7282 (m-80)
REVERT: A   64 ASN cc_start: 0.7958 (t0) cc_final: 0.7561 (t0)
REVERT: A   89 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7587 (mm-30)
REVERT: A  103 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7376 (tm-30)
REVERT: A  117 LYS cc_start: 0.8198 (mttm) cc_final: 0.7755 (mttm)
REVERT: A  168 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7771 (t0)
REVERT: A  177 LYS cc_start: 0.8286 (mttt) cc_final: 0.7983 (mmtp)
REVERT: A  201 ASN cc_start: 0.7985 (t0) cc_final: 0.7705 (t0)
REVERT: A  203 LEU cc_start: 0.8366 (mt) cc_final: 0.7994 (mp)
REVERT: A  233 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7457 (mm-30)
REVERT: A  260 ASP cc_start: 0.7924 (t0) cc_final: 0.7401 (t0)
REVERT: A  289 GLU cc_start: 0.7868 (pp20) cc_final: 0.7566 (pp20)
REVERT: A  292 ASN cc_start: 0.8037 (t0) cc_final: 0.7622 (t0)
REVERT: A  296 GLN cc_start: 0.7423 (tp-100) cc_final: 0.7172 (tp-100)
REVERT: A  323 ASN cc_start: 0.7681 (t0) cc_final: 0.7270 (t0)
REVERT: A  408 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8036 (mt)
REVERT: A  410 ASP cc_start: 0.7435 (p0) cc_final: 0.7165 (p0)
REVERT: A  412 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8362 (mtmm)
REVERT: A  436 ILE cc_start: 0.8798 (mt) cc_final: 0.8461 (tt)
REVERT: A  447 THR cc_start: 0.8673 (p) cc_final: 0.8293 (t)
REVERT: A  463 LYS cc_start: 0.8053 (tptm) cc_final: 0.7618 (tppp)
REVERT: A  469 LEU cc_start: 0.7435 (mt) cc_final: 0.7193 (mt)
REVERT: A  572 LYS cc_start: 0.8426 (mttp) cc_final: 0.8047 (mtpp)
REVERT: A  584 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7243 (mt-10)
  outliers start: 17
  outliers final: 13
  residues processed: 205
  average time/residue: 0.0919
  time to fit residues: 23.1975
Evaluate side-chains
  210 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 195
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   24 ASP
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  168 ASP
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  473 MET
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  564 ASP
Chi-restraints excluded: chain A residue  604 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.140901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.118453 restraints weight = 8011.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 2.10
r_work: 0.3374 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.3169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   5735  Z= 0.206
  Angle     :  0.599   6.933   7807  Z= 0.326
  Chirality :  0.045   0.146    876
  Planarity :  0.004   0.067    929
  Dihedral  : 15.602  66.249    885
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.08 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 19.86 %
    Favored  : 76.74 %
  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:  1.14 (0.35), residues: 624
  helix:  1.51 (0.30), residues: 302
  sheet: -0.17 (0.59), residues: 82
  loop :  0.27 (0.43), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 395 
 TYR   0.013   0.001   TYR A  42 
 PHE   0.017   0.002   PHE A 502 
 TRP   0.007   0.002   TRP A 199 
 HIS   0.003   0.001   HIS A 236 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 5735)
  covalent geometry    : angle       0.59930 ( 7807)
  hydrogen bonds       : bond        0.04187 (  290)
  hydrogen bonds       : angle       4.44484 (  801)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1296.66 seconds
wall clock time: 22 minutes 54.81 seconds (1374.81 seconds total)