Starting phenix.real_space_refine
on Tue Aug  4 18:00:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qsc_53335/08_2026/9qsc_53335.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qsc_53335/08_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qsc_53335/08_2026/9qsc_53335.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qsc_53335/08_2026/9qsc_53335.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qsc_53335/08_2026/9qsc_53335.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qsc_53335/08_2026/9qsc_53335.cif"
  }
  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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: 1.39, per 1000 atoms: 0.25
  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: 0.41
  Conformation dependent library (CDL) restraints added in 180.6 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: 0.38
  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: 0.87

  Time building geometry restraints manager: 0.58 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=" C1'  DT C  11 "
       pdb=" N1   DT C  11 "
    ideal  model  delta    sigma   weight residual
    1.468  1.542 -0.074 1.40e-02 5.10e+03 2.78e+01
  bond pdb=" C3'  DC B  15 "
       pdb=" C2'  DC B  15 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.79e+00
  bond pdb=" C3'  DC C  12 "
       pdb=" C2'  DC C  12 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 8.39e+00
  bond pdb=" C3'  DT B  22 "
       pdb=" C2'  DT B  22 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 8.27e+00
  bond pdb=" C3'  DA C  13 "
       pdb=" C2'  DA C  13 "
    ideal  model  delta    sigma   weight residual
    1.516  1.537 -0.021 8.00e-03 1.56e+04 6.71e+00
  ... (remaining 5730 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 7579
        1.41 -     2.83: 201
        2.83 -     4.24: 15
        4.24 -     5.66: 7
        5.66 -     7.07: 5
  Bond angle restraints: 7807
  Sorted by residual:
  angle pdb=" N3   DT B  19 "
        pdb=" C4   DT B  19 "
        pdb=" O4   DT B  19 "
      ideal   model   delta    sigma   weight residual
     119.90  122.31   -2.41 6.00e-01 2.78e+00 1.62e+01
  angle pdb=" N3   DT C  18 "
        pdb=" C4   DT C  18 "
        pdb=" O4   DT C  18 "
      ideal   model   delta    sigma   weight residual
     119.90  122.30   -2.40 6.00e-01 2.78e+00 1.60e+01
  angle pdb=" N3   DT B  22 "
        pdb=" C4   DT B  22 "
        pdb=" O4   DT B  22 "
      ideal   model   delta    sigma   weight residual
     119.90  122.23   -2.33 6.00e-01 2.78e+00 1.50e+01
  angle pdb=" N3   DT B  16 "
        pdb=" C4   DT B  16 "
        pdb=" O4   DT B  16 "
      ideal   model   delta    sigma   weight residual
     119.90  122.16   -2.26 6.00e-01 2.78e+00 1.42e+01
  angle pdb=" O4   DT C  18 "
        pdb=" C4   DT C  18 "
        pdb=" C5   DT C  18 "
      ideal   model   delta    sigma   weight residual
     124.90  122.29    2.61 7.00e-01 2.04e+00 1.39e+01
  ... (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 -    0.130: 866
       0.130 -    0.260: 7
       0.260 -    0.390: 0
       0.390 -    0.519: 0
       0.519 -    0.649: 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       2.34   -2.98   -0.65 2.00e-01 2.50e+01 1.05e+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       2.34   -2.91   -0.58 2.00e-01 2.50e+01 8.27e+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       2.34   -2.89   -0.56 2.00e-01 2.50e+01 7.79e+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:             0.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     6.480
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
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   0.074   5735  Z= 0.276
  Angle     :  0.566   7.069   7807  Z= 0.373
  Chirality :  0.055   0.649    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/Z
  covalent geometry    : bond        0.00444 /  0.28 ( 5735)
  covalent geometry    : angle       0.56593 /  0.37 ( 7807)
  hydrogen bonds       : bond        0.16856 / 10.86 (  290)
  hydrogen bonds       : angle       7.15022 /  4.83 (  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  : 0.211 
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: 0.0920
  time to fit residues: 24.1627
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  : 0.201 
-------------------------------------------------------------------------------
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:   20.0000
   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...
A  84 GLN
A 170 ASN
A 307 ASN
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 = 0.3839 r_free = 0.3839 target = 0.142349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.119630 restraints weight = 7964.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 2.12
r_work: 0.3393 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.1496

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= 0.192
  Angle     :  0.584   6.327   7807  Z= 0.338
  Chirality :  0.047   0.161    876
  Planarity :  0.004   0.047    929
  Dihedral  : 15.859  59.569    887
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.60 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 10.70 %
    Favored  : 87.10 %
  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:  1.01 (0.34), residues: 624
  helix:  1.32 (0.30), residues: 298
  sheet: -0.54 (0.56), residues: 74
  loop :  0.44 (0.43), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 340 
 TYR   0.023   0.002   TYR A 475 
 PHE   0.022   0.002   PHE A 502 
 TRP   0.007   0.002   TRP A 512 
 HIS   0.003   0.001   HIS A 439 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00423 /  0.19 ( 5735)
  covalent geometry    : angle       0.58376 /  0.34 ( 7807)
  hydrogen bonds       : bond        0.05705 /  3.67 (  290)
  hydrogen bonds       : angle       5.19437 /  3.59 (  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
  211 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 198
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A   17 ASP cc_start: 0.7977 (t0) cc_final: 0.7740 (t0)
REVERT: A   29 LYS cc_start: 0.8424 (mmmt) cc_final: 0.8098 (mmmt)
REVERT: A   30 ASN cc_start: 0.8219 (t0) cc_final: 0.7886 (p0)
REVERT: A   35 ILE cc_start: 0.8632 (mt) cc_final: 0.8322 (mt)
REVERT: A   47 LYS cc_start: 0.8542 (tttt) cc_final: 0.8225 (tttt)
REVERT: A   64 ASN cc_start: 0.8182 (t0) cc_final: 0.7730 (t0)
REVERT: A   89 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7675 (mm-30)
REVERT: A   97 LEU cc_start: 0.8298 (mt) cc_final: 0.8023 (mt)
REVERT: A  117 LYS cc_start: 0.8170 (mttm) cc_final: 0.7827 (mttm)
REVERT: A  136 ILE cc_start: 0.8129 (mm) cc_final: 0.7904 (mt)
REVERT: A  143 ASP cc_start: 0.7705 (m-30) cc_final: 0.7504 (m-30)
REVERT: A  201 ASN cc_start: 0.8003 (t0) cc_final: 0.7772 (t0)
REVERT: A  203 LEU cc_start: 0.8265 (mt) cc_final: 0.8060 (mp)
REVERT: A  205 ASN cc_start: 0.8021 (p0) cc_final: 0.7763 (p0)
REVERT: A  280 ASP cc_start: 0.8130 (t0) cc_final: 0.7759 (t0)
REVERT: A  292 ASN cc_start: 0.7884 (t0) cc_final: 0.7533 (t0)
REVERT: A  319 THR cc_start: 0.7625 (p) cc_final: 0.7342 (p)
REVERT: A  339 TYR cc_start: 0.8484 (t80) cc_final: 0.8213 (t80)
REVERT: A  380 SER cc_start: 0.8284 (p) cc_final: 0.8007 (p)
REVERT: A  410 ASP cc_start: 0.7395 (p0) cc_final: 0.7168 (p0)
REVERT: A  412 LYS cc_start: 0.8702 (mtmt) cc_final: 0.8358 (mtmm)
REVERT: A  430 LYS cc_start: 0.8478 (ttpp) cc_final: 0.8212 (ttmm)
REVERT: A  447 THR cc_start: 0.8686 (p) cc_final: 0.8278 (t)
REVERT: A  463 LYS cc_start: 0.7974 (tptm) cc_final: 0.7456 (tppp)
REVERT: A  477 ASN cc_start: 0.7804 (t0) cc_final: 0.7575 (t0)
REVERT: A  479 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7870 (tptt)
REVERT: A  490 MET cc_start: 0.7790 (mmm) cc_final: 0.7525 (mmm)
REVERT: A  517 LYS cc_start: 0.8468 (ttmt) cc_final: 0.8109 (ttmm)
REVERT: A  575 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8336 (mt)
REVERT: A  580 GLU cc_start: 0.8218 (tt0) cc_final: 0.7990 (tt0)
  outliers start: 13
  outliers final: 7
  residues processed: 204
  average time/residue: 0.0784
  time to fit residues: 20.0759
Evaluate side-chains
  201 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 192
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  287 LYS
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  479 LYS
Chi-restraints excluded: chain A residue  575 LEU
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:    1.9990
   chunk 15 optimal weight:    0.0970
   chunk 40 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 43 optimal weight:    0.0980
   overall best weight:    0.4378

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  84 GLN
A 139 ASN
A 170 ASN
A 297 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.143683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.120735 restraints weight = 7901.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 2.11
r_work: 0.3413 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5735  Z= 0.140
  Angle     :  0.525   6.069   7807  Z= 0.307
  Chirality :  0.045   0.140    876
  Planarity :  0.004   0.052    929
  Dihedral  : 15.864  59.552    885
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.76 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 13.07 %
    Favored  : 84.38 %
  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:  1.49 (0.30), residues: 298
  sheet: -0.36 (0.59), residues: 72
  loop :  0.24 (0.41), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 395 
 TYR   0.029   0.001   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 513 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.14 ( 5735)
  covalent geometry    : angle       0.52470 /  0.31 ( 7807)
  hydrogen bonds       : bond        0.04683 /  3.04 (  290)
  hydrogen bonds       : angle       4.90789 /  3.40 (  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
  213 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 198
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8640 (mmmt) cc_final: 0.8355 (tppt)
REVERT: A   30 ASN cc_start: 0.8242 (t0) cc_final: 0.8030 (t0)
REVERT: A   36 THR cc_start: 0.8692 (t) cc_final: 0.8286 (p)
REVERT: A   64 ASN cc_start: 0.8372 (t0) cc_final: 0.7930 (t0)
REVERT: A   74 LYS cc_start: 0.8550 (ttmt) cc_final: 0.8308 (tptp)
REVERT: A   89 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7924 (mm-30)
REVERT: A   96 ARG cc_start: 0.8066 (tpt90) cc_final: 0.7833 (tpt170)
REVERT: A  117 LYS cc_start: 0.8172 (mttm) cc_final: 0.7809 (mttm)
REVERT: A  136 ILE cc_start: 0.8268 (mm) cc_final: 0.8061 (mt)
REVERT: A  201 ASN cc_start: 0.8182 (t0) cc_final: 0.7850 (t0)
REVERT: A  203 LEU cc_start: 0.8314 (mt) cc_final: 0.8091 (mp)
REVERT: A  233 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7684 (mm-30)
REVERT: A  280 ASP cc_start: 0.8313 (t0) cc_final: 0.7966 (t0)
REVERT: A  285 LYS cc_start: 0.8146 (mttm) cc_final: 0.7637 (mttm)
REVERT: A  286 LEU cc_start: 0.9028 (mt) cc_final: 0.8773 (mp)
REVERT: A  292 ASN cc_start: 0.7940 (t0) cc_final: 0.7428 (t0)
REVERT: A  319 THR cc_start: 0.7645 (p) cc_final: 0.7178 (p)
REVERT: A  332 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7994 (mm-30)
REVERT: A  380 SER cc_start: 0.8283 (p) cc_final: 0.7998 (p)
REVERT: A  410 ASP cc_start: 0.7634 (p0) cc_final: 0.7393 (p0)
REVERT: A  412 LYS cc_start: 0.8789 (mtmt) cc_final: 0.8453 (mtmm)
REVERT: A  425 ASP cc_start: 0.7859 (t0) cc_final: 0.7635 (t0)
REVERT: A  430 LYS cc_start: 0.8516 (ttpp) cc_final: 0.8254 (ttmm)
REVERT: A  447 THR cc_start: 0.8827 (p) cc_final: 0.8436 (t)
REVERT: A  463 LYS cc_start: 0.8086 (tptm) cc_final: 0.7599 (tppp)
REVERT: A  490 MET cc_start: 0.8199 (mmm) cc_final: 0.7847 (mmm)
REVERT: A  517 LYS cc_start: 0.8514 (ttmt) cc_final: 0.8165 (ttmm)
REVERT: A  580 GLU cc_start: 0.8270 (tt0) cc_final: 0.7961 (tt0)
  outliers start: 15
  outliers final: 8
  residues processed: 203
  average time/residue: 0.0787
  time to fit residues: 19.6898
Evaluate side-chains
  198 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 190
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
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  170 ASN
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  289 GLU
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=4.00
-------------------------------------------------------------------------------
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:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0970
   chunk 16 optimal weight:    1.9990
   chunk 62 optimal weight:   20.0000
   chunk 34 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.6778

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 170 ASN
A 318 ASN
A 413 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.142817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.119889 restraints weight = 7915.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 2.08
r_work: 0.3402 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3243 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.2075

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= 0.170
  Angle     :  0.535   5.915   7807  Z= 0.310
  Chirality :  0.045   0.140    876
  Planarity :  0.004   0.053    929
  Dihedral  : 15.917  59.971    885
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.76 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 16.13 %
    Favored  : 81.83 %
  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:  1.06 (0.34), residues: 624
  helix:  1.48 (0.30), residues: 302
  sheet: -0.28 (0.60), residues: 72
  loop :  0.20 (0.42), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 395 
 TYR   0.027   0.001   TYR A  65 
 PHE   0.016   0.002   PHE A 502 
 TRP   0.005   0.001   TRP A 512 
 HIS   0.003   0.001   HIS A 505 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00377 /  0.17 ( 5735)
  covalent geometry    : angle       0.53469 /  0.31 ( 7807)
  hydrogen bonds       : bond        0.04546 /  2.94 (  290)
  hydrogen bonds       : angle       4.79628 /  3.32 (  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
  205 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 193
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8675 (mmmt) cc_final: 0.8365 (tppt)
REVERT: A   30 ASN cc_start: 0.8209 (t0) cc_final: 0.7668 (p0)
REVERT: A   36 THR cc_start: 0.8642 (t) cc_final: 0.8233 (p)
REVERT: A   64 ASN cc_start: 0.8393 (t0) cc_final: 0.8066 (t0)
REVERT: A   74 LYS cc_start: 0.8513 (ttmt) cc_final: 0.8267 (tptp)
REVERT: A   89 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7906 (mm-30)
REVERT: A  117 LYS cc_start: 0.8171 (mttm) cc_final: 0.7817 (mttm)
REVERT: A  136 ILE cc_start: 0.8268 (mm) cc_final: 0.8066 (mt)
REVERT: A  201 ASN cc_start: 0.8200 (t0) cc_final: 0.7956 (t0)
REVERT: A  203 LEU cc_start: 0.8289 (mt) cc_final: 0.8067 (mp)
REVERT: A  233 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7660 (mm-30)
REVERT: A  280 ASP cc_start: 0.8351 (t0) cc_final: 0.7997 (t0)
REVERT: A  285 LYS cc_start: 0.8208 (mttm) cc_final: 0.7714 (mttm)
REVERT: A  292 ASN cc_start: 0.8021 (t0) cc_final: 0.7783 (t0)
REVERT: A  293 VAL cc_start: 0.8480 (t) cc_final: 0.8276 (p)
REVERT: A  319 THR cc_start: 0.7716 (p) cc_final: 0.7416 (p)
REVERT: A  332 GLU cc_start: 0.8226 (mm-30) cc_final: 0.8009 (tp30)
REVERT: A  340 ARG cc_start: 0.8730 (tpp80) cc_final: 0.8442 (tpp80)
REVERT: A  380 SER cc_start: 0.8190 (p) cc_final: 0.7857 (p)
REVERT: A  410 ASP cc_start: 0.7597 (p0) cc_final: 0.7339 (p0)
REVERT: A  412 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8403 (mtmm)
REVERT: A  425 ASP cc_start: 0.7897 (t0) cc_final: 0.7619 (t0)
REVERT: A  430 LYS cc_start: 0.8509 (ttpp) cc_final: 0.8262 (ttmm)
REVERT: A  463 LYS cc_start: 0.8146 (tptm) cc_final: 0.7757 (tptm)
REVERT: A  490 MET cc_start: 0.8148 (mmm) cc_final: 0.7804 (mmm)
REVERT: A  517 LYS cc_start: 0.8484 (ttmt) cc_final: 0.8085 (ttmm)
REVERT: A  580 GLU cc_start: 0.8268 (tt0) cc_final: 0.7922 (tt0)
REVERT: A  584 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7624 (mt-10)
  outliers start: 12
  outliers final: 9
  residues processed: 196
  average time/residue: 0.1006
  time to fit residues: 24.3611
Evaluate side-chains
  197 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 188
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
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  172 ASN
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  289 GLU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 62 optimal weight:   20.0000
   overall best weight:    1.0382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 170 ASN
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 297 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.141488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.118384 restraints weight = 7954.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 2.14
r_work: 0.3372 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   5735  Z= 0.222
  Angle     :  0.563   6.852   7807  Z= 0.319
  Chirality :  0.046   0.144    876
  Planarity :  0.003   0.055    929
  Dihedral  : 15.931  59.156    885
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.08 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.64 %
    Favored  : 80.65 %
  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:  1.00 (0.34), residues: 624
  helix:  1.43 (0.30), residues: 302
  sheet: -0.33 (0.59), residues: 74
  loop :  0.18 (0.42), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 340 
 TYR   0.011   0.001   TYR A  65 
 PHE   0.017   0.002   PHE A  58 
 TRP   0.005   0.002   TRP A 199 
 HIS   0.002   0.001   HIS A 330 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00506 /  0.22 ( 5735)
  covalent geometry    : angle       0.56268 /  0.32 ( 7807)
  hydrogen bonds       : bond        0.04751 /  3.05 (  290)
  hydrogen bonds       : angle       4.78673 /  3.32 (  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
  207 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 191
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8511 (mmmt) cc_final: 0.8216 (tppt)
REVERT: A   29 LYS cc_start: 0.8285 (mmmt) cc_final: 0.8083 (mmmt)
REVERT: A   36 THR cc_start: 0.8641 (t) cc_final: 0.8236 (p)
REVERT: A   64 ASN cc_start: 0.8146 (t0) cc_final: 0.7942 (t0)
REVERT: A   74 LYS cc_start: 0.8483 (ttmt) cc_final: 0.8212 (tptp)
REVERT: A   89 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7622 (mm-30)
REVERT: A  117 LYS cc_start: 0.8171 (mttm) cc_final: 0.7822 (mttm)
REVERT: A  177 LYS cc_start: 0.8179 (mttp) cc_final: 0.7943 (mttt)
REVERT: A  201 ASN cc_start: 0.8077 (t0) cc_final: 0.7827 (t0)
REVERT: A  203 LEU cc_start: 0.8306 (mt) cc_final: 0.8074 (mp)
REVERT: A  233 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7553 (mm-30)
REVERT: A  260 ASP cc_start: 0.7927 (t0) cc_final: 0.7368 (t0)
REVERT: A  280 ASP cc_start: 0.8165 (t0) cc_final: 0.7769 (t0)
REVERT: A  292 ASN cc_start: 0.8041 (t0) cc_final: 0.7503 (t0)
REVERT: A  293 VAL cc_start: 0.8489 (t) cc_final: 0.8193 (p)
REVERT: A  319 THR cc_start: 0.7830 (p) cc_final: 0.7500 (p)
REVERT: A  377 ARG cc_start: 0.8425 (mtp180) cc_final: 0.8210 (mtp180)
REVERT: A  380 SER cc_start: 0.8209 (p) cc_final: 0.7890 (p)
REVERT: A  410 ASP cc_start: 0.7462 (p0) cc_final: 0.7208 (p0)
REVERT: A  412 LYS cc_start: 0.8712 (mtmt) cc_final: 0.8329 (mtmm)
REVERT: A  425 ASP cc_start: 0.7662 (t0) cc_final: 0.7417 (t0)
REVERT: A  430 LYS cc_start: 0.8479 (ttpp) cc_final: 0.8251 (ttmm)
REVERT: A  463 LYS cc_start: 0.8091 (tptm) cc_final: 0.7727 (tptm)
REVERT: A  474 ASN cc_start: 0.8209 (t0) cc_final: 0.7911 (t0)
REVERT: A  580 GLU cc_start: 0.8211 (tt0) cc_final: 0.7985 (tt0)
REVERT: A  584 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7236 (mt-10)
  outliers start: 16
  outliers final: 12
  residues processed: 196
  average time/residue: 0.0943
  time to fit residues: 23.1213
Evaluate side-chains
  198 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 186
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
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   51 ASP
Chi-restraints excluded: chain A residue  129 GLU
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  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:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0470
   chunk 39 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0170
   chunk 5 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.5518

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 170 ASN
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 265 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.142486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.119316 restraints weight = 7891.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 2.13
r_work: 0.3389 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.2336

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= 0.155
  Angle     :  0.550   8.400   7807  Z= 0.311
  Chirality :  0.044   0.151    876
  Planarity :  0.003   0.056    929
  Dihedral  : 15.916  58.595    885
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.76 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 17.32 %
    Favored  : 79.46 %
  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:  0.96 (0.34), residues: 624
  helix:  1.46 (0.30), residues: 301
  sheet: -0.33 (0.60), residues: 74
  loop :  0.05 (0.40), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 340 
 TYR   0.008   0.001   TYR A 161 
 PHE   0.028   0.002   PHE A 537 
 TRP   0.005   0.001   TRP A 512 
 HIS   0.002   0.001   HIS A 513 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.16 ( 5735)
  covalent geometry    : angle       0.54998 /  0.31 ( 7807)
  hydrogen bonds       : bond        0.04450 /  2.86 (  290)
  hydrogen bonds       : angle       4.72212 /  3.28 (  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
  209 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 190
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8505 (mmmt) cc_final: 0.8209 (tppt)
REVERT: A   64 ASN cc_start: 0.8104 (t0) cc_final: 0.7886 (t0)
REVERT: A   89 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7575 (mm-30)
REVERT: A  117 LYS cc_start: 0.8180 (mttm) cc_final: 0.7820 (mttm)
REVERT: A  201 ASN cc_start: 0.8089 (t0) cc_final: 0.7825 (t0)
REVERT: A  203 LEU cc_start: 0.8306 (mt) cc_final: 0.8075 (mp)
REVERT: A  233 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7563 (mm-30)
REVERT: A  260 ASP cc_start: 0.7908 (t0) cc_final: 0.7343 (t0)
REVERT: A  280 ASP cc_start: 0.8082 (t0) cc_final: 0.7678 (t0)
REVERT: A  285 LYS cc_start: 0.8009 (mttm) cc_final: 0.7489 (mttm)
REVERT: A  286 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8603 (mp)
REVERT: A  292 ASN cc_start: 0.7992 (t0) cc_final: 0.7508 (t0)
REVERT: A  293 VAL cc_start: 0.8458 (t) cc_final: 0.8171 (p)
REVERT: A  319 THR cc_start: 0.7818 (p) cc_final: 0.7458 (p)
REVERT: A  332 GLU cc_start: 0.7880 (tp30) cc_final: 0.7482 (mm-30)
REVERT: A  336 LEU cc_start: 0.8399 (tp) cc_final: 0.8190 (tt)
REVERT: A  377 ARG cc_start: 0.8401 (mtp180) cc_final: 0.8148 (mtp180)
REVERT: A  380 SER cc_start: 0.8195 (p) cc_final: 0.7876 (p)
REVERT: A  410 ASP cc_start: 0.7407 (p0) cc_final: 0.7182 (p0)
REVERT: A  412 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8311 (mtmm)
REVERT: A  428 MET cc_start: 0.8268 (mtt) cc_final: 0.7966 (mtt)
REVERT: A  430 LYS cc_start: 0.8465 (ttpp) cc_final: 0.8233 (ttmm)
REVERT: A  463 LYS cc_start: 0.8045 (tptm) cc_final: 0.7673 (tptm)
REVERT: A  474 ASN cc_start: 0.8199 (t0) cc_final: 0.7828 (t0)
REVERT: A  490 MET cc_start: 0.7649 (mmm) cc_final: 0.7260 (mmm)
REVERT: A  580 GLU cc_start: 0.8211 (tt0) cc_final: 0.7980 (tt0)
REVERT: A  584 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7238 (mt-10)
  outliers start: 19
  outliers final: 13
  residues processed: 197
  average time/residue: 0.0983
  time to fit residues: 23.9987
Evaluate side-chains
  205 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 191
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
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   51 ASP
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  168 ASP
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  286 LEU
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  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:    0.9990
   chunk 43 optimal weight:    0.1980
   chunk 48 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0770
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.6138

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 170 ASN
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.142482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.119298 restraints weight = 8024.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 2.12
r_work: 0.3391 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.2444

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= 0.159
  Angle     :  0.547   7.166   7807  Z= 0.309
  Chirality :  0.045   0.162    876
  Planarity :  0.003   0.055    929
  Dihedral  : 15.883  59.355    885
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.92 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 17.15 %
    Favored  : 78.78 %
  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:  1.00 (0.34), residues: 624
  helix:  1.52 (0.30), residues: 301
  sheet: -0.29 (0.60), residues: 74
  loop :  0.03 (0.41), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 340 
 TYR   0.028   0.001   TYR A 475 
 PHE   0.015   0.002   PHE A  58 
 TRP   0.005   0.001   TRP A 512 
 HIS   0.002   0.001   HIS A 439 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.16 ( 5735)
  covalent geometry    : angle       0.54697 /  0.31 ( 7807)
  hydrogen bonds       : bond        0.04331 /  2.77 (  290)
  hydrogen bonds       : angle       4.64895 /  3.23 (  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
  219 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 195
  time to evaluate  : 0.256 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8499 (mmmt) cc_final: 0.8224 (tppt)
REVERT: A   29 LYS cc_start: 0.8203 (mmmt) cc_final: 0.7935 (mmmm)
REVERT: A   30 ASN cc_start: 0.8056 (t0) cc_final: 0.7700 (p0)
REVERT: A   64 ASN cc_start: 0.8104 (t0) cc_final: 0.7823 (t0)
REVERT: A   89 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7573 (mm-30)
REVERT: A   96 ARG cc_start: 0.7954 (tpt90) cc_final: 0.7598 (tpt-90)
REVERT: A  103 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7221 (tm-30)
REVERT: A  117 LYS cc_start: 0.8201 (mttm) cc_final: 0.7767 (mttm)
REVERT: A  201 ASN cc_start: 0.8108 (t0) cc_final: 0.7479 (t0)
REVERT: A  203 LEU cc_start: 0.8315 (mt) cc_final: 0.8040 (mp)
REVERT: A  233 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7493 (mm-30)
REVERT: A  260 ASP cc_start: 0.7882 (t0) cc_final: 0.7306 (t0)
REVERT: A  286 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8690 (mp)
REVERT: A  292 ASN cc_start: 0.7996 (t0) cc_final: 0.7499 (t0)
REVERT: A  293 VAL cc_start: 0.8451 (t) cc_final: 0.8163 (p)
REVERT: A  319 THR cc_start: 0.7855 (p) cc_final: 0.7493 (p)
REVERT: A  336 LEU cc_start: 0.8429 (tp) cc_final: 0.8225 (tt)
REVERT: A  380 SER cc_start: 0.8182 (p) cc_final: 0.7834 (p)
REVERT: A  410 ASP cc_start: 0.7418 (p0) cc_final: 0.7192 (p0)
REVERT: A  412 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8319 (mtmm)
REVERT: A  430 LYS cc_start: 0.8467 (ttpp) cc_final: 0.8239 (ttmm)
REVERT: A  463 LYS cc_start: 0.8048 (tptm) cc_final: 0.7680 (ttmm)
REVERT: A  474 ASN cc_start: 0.8206 (t0) cc_final: 0.7815 (t0)
REVERT: A  490 MET cc_start: 0.7679 (mmm) cc_final: 0.7312 (mmm)
REVERT: A  580 GLU cc_start: 0.8212 (tt0) cc_final: 0.7922 (tt0)
REVERT: A  584 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7243 (mt-10)
  outliers start: 24
  outliers final: 15
  residues processed: 202
  average time/residue: 0.0963
  time to fit residues: 24.1914
Evaluate side-chains
  208 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 192
  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   51 ASP
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  249 ILE
Chi-restraints excluded: chain A residue  286 LEU
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  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:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0970
   chunk 10 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.6578

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 139 ASN
A 170 ASN
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 297 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.142612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.119574 restraints weight = 7907.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 2.10
r_work: 0.3382 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2523

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= 0.166
  Angle     :  0.551   6.297   7807  Z= 0.311
  Chirality :  0.045   0.158    876
  Planarity :  0.003   0.057    929
  Dihedral  : 15.830  59.748    885
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.76 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 17.83 %
    Favored  : 78.61 %
  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:  0.95 (0.34), residues: 624
  helix:  1.49 (0.30), residues: 301
  sheet: -0.28 (0.60), residues: 74
  loop : -0.02 (0.40), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 340 
 TYR   0.027   0.001   TYR A 475 
 PHE   0.015   0.002   PHE A  58 
 TRP   0.005   0.001   TRP A 199 
 HIS   0.002   0.001   HIS A 439 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00376 /  0.17 ( 5735)
  covalent geometry    : angle       0.55123 /  0.31 ( 7807)
  hydrogen bonds       : bond        0.04354 /  2.79 (  290)
  hydrogen bonds       : angle       4.63577 /  3.23 (  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
  216 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 195
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8655 (mmmt) cc_final: 0.8375 (tppt)
REVERT: A   29 LYS cc_start: 0.8294 (mmmt) cc_final: 0.8017 (mmmm)
REVERT: A   64 ASN cc_start: 0.8373 (t0) cc_final: 0.8119 (t0)
REVERT: A   89 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7907 (mm-30)
REVERT: A  103 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7505 (tm-30)
REVERT: A  117 LYS cc_start: 0.8304 (mttm) cc_final: 0.7878 (mttm)
REVERT: A  201 ASN cc_start: 0.8276 (t0) cc_final: 0.8009 (t0)
REVERT: A  203 LEU cc_start: 0.8368 (mt) cc_final: 0.8125 (mp)
REVERT: A  233 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7675 (mm-30)
REVERT: A  260 ASP cc_start: 0.8029 (t0) cc_final: 0.7451 (t0)
REVERT: A  292 ASN cc_start: 0.8143 (t0) cc_final: 0.7718 (t0)
REVERT: A  319 THR cc_start: 0.7821 (p) cc_final: 0.7427 (p)
REVERT: A  323 ASN cc_start: 0.7598 (t0) cc_final: 0.7111 (t0)
REVERT: A  336 LEU cc_start: 0.8570 (tp) cc_final: 0.8356 (tt)
REVERT: A  380 SER cc_start: 0.8247 (p) cc_final: 0.7879 (p)
REVERT: A  410 ASP cc_start: 0.7672 (p0) cc_final: 0.7435 (p0)
REVERT: A  412 LYS cc_start: 0.8788 (mtmt) cc_final: 0.8428 (mtmm)
REVERT: A  430 LYS cc_start: 0.8575 (ttpp) cc_final: 0.8361 (ttmm)
REVERT: A  436 ILE cc_start: 0.8885 (mt) cc_final: 0.8516 (tt)
REVERT: A  463 LYS cc_start: 0.8200 (tptm) cc_final: 0.7856 (ttmm)
REVERT: A  490 MET cc_start: 0.8142 (mmm) cc_final: 0.7628 (mmm)
REVERT: A  580 GLU cc_start: 0.8318 (tt0) cc_final: 0.8101 (tt0)
REVERT: A  584 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7609 (mt-10)
  outliers start: 21
  outliers final: 16
  residues processed: 200
  average time/residue: 0.1026
  time to fit residues: 25.4448
Evaluate side-chains
  209 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 193
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
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   51 ASP
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  168 ASP
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  296 GLN
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  473 MET
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:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 139 ASN
A 170 ASN
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 298 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.141643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.118634 restraints weight = 7896.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 2.08
r_work: 0.3381 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3217 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5735  Z= 0.186
  Angle     :  0.558   5.889   7807  Z= 0.316
  Chirality :  0.045   0.147    876
  Planarity :  0.003   0.057    929
  Dihedral  : 15.756  58.662    885
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.92 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 17.66 %
    Favored  : 78.78 %
  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:  0.95 (0.34), residues: 624
  helix:  1.47 (0.30), residues: 302
  sheet: -0.24 (0.60), residues: 74
  loop : -0.02 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 340 
 TYR   0.027   0.001   TYR A 475 
 PHE   0.016   0.002   PHE A  58 
 TRP   0.005   0.001   TRP A 199 
 HIS   0.002   0.001   HIS A 439 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00423 /  0.19 ( 5735)
  covalent geometry    : angle       0.55816 /  0.32 ( 7807)
  hydrogen bonds       : bond        0.04453 /  2.84 (  290)
  hydrogen bonds       : angle       4.60205 /  3.21 (  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: 21
    poor density    : 197
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8681 (mmmt) cc_final: 0.8381 (tppt)
REVERT: A   29 LYS cc_start: 0.8273 (mmmt) cc_final: 0.8000 (mmmm)
REVERT: A   64 ASN cc_start: 0.8402 (t0) cc_final: 0.8150 (t0)
REVERT: A   89 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7915 (mm-30)
REVERT: A  103 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7525 (tm-30)
REVERT: A  117 LYS cc_start: 0.8302 (mttm) cc_final: 0.7867 (mttm)
REVERT: A  201 ASN cc_start: 0.8283 (t0) cc_final: 0.8006 (t0)
REVERT: A  203 LEU cc_start: 0.8365 (mt) cc_final: 0.8108 (mp)
REVERT: A  233 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7683 (mm-30)
REVERT: A  260 ASP cc_start: 0.8041 (t0) cc_final: 0.7459 (t0)
REVERT: A  292 ASN cc_start: 0.8186 (t0) cc_final: 0.7730 (t0)
REVERT: A  319 THR cc_start: 0.7809 (p) cc_final: 0.7417 (p)
REVERT: A  323 ASN cc_start: 0.7609 (t0) cc_final: 0.7152 (t0)
REVERT: A  336 LEU cc_start: 0.8582 (tp) cc_final: 0.8343 (tt)
REVERT: A  380 SER cc_start: 0.8220 (p) cc_final: 0.7839 (p)
REVERT: A  410 ASP cc_start: 0.7682 (p0) cc_final: 0.7448 (p0)
REVERT: A  412 LYS cc_start: 0.8798 (mtmt) cc_final: 0.8442 (mtmm)
REVERT: A  425 ASP cc_start: 0.7865 (t0) cc_final: 0.7625 (t0)
REVERT: A  430 LYS cc_start: 0.8592 (ttpp) cc_final: 0.8366 (ttmm)
REVERT: A  436 ILE cc_start: 0.8889 (mt) cc_final: 0.8527 (tt)
REVERT: A  463 LYS cc_start: 0.8223 (tptm) cc_final: 0.7754 (tppp)
REVERT: A  490 MET cc_start: 0.8143 (mmm) cc_final: 0.7652 (mmm)
REVERT: A  572 LYS cc_start: 0.8454 (mttp) cc_final: 0.8080 (mtpp)
REVERT: A  580 GLU cc_start: 0.8312 (tt0) cc_final: 0.8088 (tt0)
REVERT: A  584 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7594 (mt-10)
  outliers start: 21
  outliers final: 16
  residues processed: 203
  average time/residue: 0.0968
  time to fit residues: 24.3372
Evaluate side-chains
  209 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 193
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
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   51 ASP
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  249 ILE
Chi-restraints excluded: chain A residue  296 GLN
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  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:    0.5980
   chunk 41 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0770
   chunk 47 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.5138

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 139 ASN
A 170 ASN
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 298 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.142663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.119563 restraints weight = 7997.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 2.12
r_work: 0.3394 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3230 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5735  Z= 0.145
  Angle     :  0.558   7.005   7807  Z= 0.313
  Chirality :  0.045   0.149    876
  Planarity :  0.003   0.054    929
  Dihedral  : 15.742  58.602    885
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.92 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 18.51 %
    Favored  : 78.44 %
  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:  1.01 (0.34), residues: 624
  helix:  1.55 (0.30), residues: 302
  sheet: -0.22 (0.60), residues: 74
  loop : -0.03 (0.41), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 340 
 TYR   0.028   0.001   TYR A 475 
 PHE   0.014   0.002   PHE A  58 
 TRP   0.005   0.001   TRP A 199 
 HIS   0.002   0.001   HIS A 513 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.15 ( 5735)
  covalent geometry    : angle       0.55843 /  0.31 ( 7807)
  hydrogen bonds       : bond        0.04194 /  2.67 (  290)
  hydrogen bonds       : angle       4.56807 /  3.19 (  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
  217 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 199
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8695 (mmmt) cc_final: 0.8380 (tppt)
REVERT: A   29 LYS cc_start: 0.8262 (mmmt) cc_final: 0.7996 (mmmm)
REVERT: A   64 ASN cc_start: 0.8391 (t0) cc_final: 0.7896 (t0)
REVERT: A   68 ASN cc_start: 0.8595 (m-40) cc_final: 0.8331 (m110)
REVERT: A   89 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7890 (mm-30)
REVERT: A  103 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7621 (tm-30)
REVERT: A  117 LYS cc_start: 0.8276 (mttm) cc_final: 0.7831 (mttm)
REVERT: A  201 ASN cc_start: 0.8261 (t0) cc_final: 0.7988 (t0)
REVERT: A  203 LEU cc_start: 0.8380 (mt) cc_final: 0.8104 (mp)
REVERT: A  233 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7672 (mm-30)
REVERT: A  260 ASP cc_start: 0.8037 (t0) cc_final: 0.7516 (t0)
REVERT: A  292 ASN cc_start: 0.8147 (t0) cc_final: 0.7757 (t0)
REVERT: A  293 VAL cc_start: 0.8499 (t) cc_final: 0.8225 (p)
REVERT: A  319 THR cc_start: 0.7813 (p) cc_final: 0.7418 (p)
REVERT: A  323 ASN cc_start: 0.7624 (t0) cc_final: 0.7184 (t0)
REVERT: A  336 LEU cc_start: 0.8505 (tp) cc_final: 0.8297 (tt)
REVERT: A  377 ARG cc_start: 0.8475 (mtp85) cc_final: 0.8214 (mtp85)
REVERT: A  380 SER cc_start: 0.8170 (p) cc_final: 0.7733 (p)
REVERT: A  410 ASP cc_start: 0.7690 (p0) cc_final: 0.7450 (p0)
REVERT: A  412 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8425 (mtmm)
REVERT: A  430 LYS cc_start: 0.8570 (ttpp) cc_final: 0.8334 (ttmm)
REVERT: A  436 ILE cc_start: 0.8893 (mt) cc_final: 0.8528 (tt)
REVERT: A  463 LYS cc_start: 0.8201 (tptm) cc_final: 0.7717 (tppp)
REVERT: A  490 MET cc_start: 0.8060 (mmm) cc_final: 0.7639 (mmm)
REVERT: A  572 LYS cc_start: 0.8453 (mttp) cc_final: 0.8087 (mtpp)
REVERT: A  580 GLU cc_start: 0.8302 (tt0) cc_final: 0.8075 (tt0)
REVERT: A  584 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7616 (mt-10)
  outliers start: 18
  outliers final: 15
  residues processed: 204
  average time/residue: 0.0851
  time to fit residues: 21.6111
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  : 0.119 
-------------------------------------------------------------------------------
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   51 ASP
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  296 GLN
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  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 17 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 2 optimal weight:    0.4980
   chunk 27 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 139 ASN
A 170 ASN
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.141964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.118973 restraints weight = 7898.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.13
r_work: 0.3388 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2709

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= 0.162
  Angle     :  0.567   6.839   7807  Z= 0.317
  Chirality :  0.045   0.153    876
  Planarity :  0.003   0.056    929
  Dihedral  : 15.764  58.550    885
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.76 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 18.17 %
    Favored  : 78.44 %
  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:  0.97 (0.35), residues: 624
  helix:  1.52 (0.30), residues: 302
  sheet: -0.34 (0.56), residues: 87
  loop :  0.02 (0.43), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 340 
 TYR   0.028   0.001   TYR A 475 
 PHE   0.015   0.002   PHE A  58 
 TRP   0.005   0.001   TRP A 199 
 HIS   0.002   0.001   HIS A 439 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.16 ( 5735)
  covalent geometry    : angle       0.56706 /  0.32 ( 7807)
  hydrogen bonds       : bond        0.04230 /  2.69 (  290)
  hydrogen bonds       : angle       4.57159 /  3.19 (  801)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1394.42 seconds
wall clock time: 24 minutes 37.43 seconds (1477.43 seconds total)