Starting phenix.real_space_refine
on Fri May  9 16:47:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wma_37647/05_2025/8wma_37647_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wma_37647/05_2025/8wma_37647.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wma_37647/05_2025/8wma_37647.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wma_37647/05_2025/8wma_37647.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wma_37647/05_2025/8wma_37647_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wma_37647/05_2025/8wma_37647_neut.cif"
  }
  resolution = 3.47
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      21      5.16       5
     C    2089      2.51       5
     N     506      2.21       5
     O     556      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3172
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2490
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 2490
          Classifications: {'peptide': 323}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 316}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 98
          Unresolved non-hydrogen angles: 120
          Unresolved non-hydrogen dihedrals: 81
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 62
    Chain: "C"
      Number of atoms: 682
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 682
          Classifications: {'peptide': 90}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 3, 'TRANS': 86}
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 33
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 29
  Time building chain proxies: 2.77, per 1000 atoms: 0.87
  Number of scatterers: 3172
  At special positions: 0
  Unit cell: (89.1, 99, 51.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      21     16.00
     O     556      8.00
     N     506      7.00
     C    2089      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 204 " - pdb=" SG  CYS A 282 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 302 " - pdb=" SG  CYS A 377 " distance=2.05

  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: 0.94
  Conformation dependent library (CDL) restraints added in 397.0 milliseconds
  

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  780

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 3 sheets defined
      67.8% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 212 through 244
      removed outlier: 3.798A  pdb=" N   ASP A 244 " --> pdb=" O   THR A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 276
      removed outlier: 3.960A  pdb=" N   PHE A 257 " --> pdb=" O   ARG A 253 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   TYR A 269 " --> pdb=" O   TYR A 265 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ILE A 270 " --> pdb=" O   SER A 266 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   ARG A 272 " --> pdb=" O   ALA A 268 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LEU A 273 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 281
    Processing helix  chain 'A' and resid 295 through 298
      removed outlier: 3.584A  pdb=" N   LYS A 298 " --> pdb=" O   GLU A 295 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 295 through 298'
    Processing helix  chain 'A' and resid 299 through 332
      removed outlier: 3.796A  pdb=" N   ALA A 303 " --> pdb=" O   ASN A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 342
      No H-bonds generated for 'chain 'A' and resid 340 through 342'
    Processing helix  chain 'A' and resid 343 through 366
      Proline residue:  A 355  - end of helix
    Processing helix  chain 'A' and resid 383 through 391
      removed outlier: 3.538A  pdb=" N   LEU A 387 " --> pdb=" O   ASN A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 422
      removed outlier: 3.879A  pdb=" N   LEU A 395 " --> pdb=" O   VAL A 391 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   LYS A 422 " --> pdb=" O   SER A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 461
      removed outlier: 3.839A  pdb=" N   GLU A 431 " --> pdb=" O   THR A 427 " (cutoff:3.500A)
      Proline residue:  A 447  - end of helix
    Processing helix  chain 'A' and resid 461 through 467
      removed outlier: 3.889A  pdb=" N   PHE A 465 " --> pdb=" O   ASN A 461 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   ARG A 466 " --> pdb=" O   TRP A 462 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   TYR A 467 " --> pdb=" O   ALA A 463 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 461 through 467'
    Processing helix  chain 'A' and resid 470 through 490
      removed outlier: 4.092A  pdb=" N   MET A 474 " --> pdb=" O   ASP A 470 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ALA A 475 " --> pdb=" O   ASP A 471 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   VAL A 487 " --> pdb=" O   MET A 483 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   GLY A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 511
      removed outlier: 3.595A  pdb=" N   LEU A 511 " --> pdb=" O   PHE A 507 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 422 through 431
    Processing helix  chain 'C' and resid 455 through 465
    Processing helix  chain 'C' and resid 474 through 485
      removed outlier: 3.743A  pdb=" N   TYR C 478 " --> pdb=" O   GLU C 474 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ALA C 479 " --> pdb=" O   ALA C 475 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   SER C 480 " --> pdb=" O   ARG C 476 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 194
    Processing sheet with id=AA2, first strand: chain 'A' and resid 369 through 370
    Processing sheet with id=AA3, first strand: chain 'C' and resid 440 through 444
      removed outlier: 5.683A  pdb=" N   ARG C 440 " --> pdb=" O   ASN C 451 " (cutoff:3.500A)
      removed outlier: 8.856A  pdb=" N   ASN C 451 " --> pdb=" O   PHE C 505 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   PHE C 505 " --> pdb=" O   ASN C 451 " (cutoff:3.500A)

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

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 955
        1.35 -     1.47: 910
        1.47 -     1.59: 1357
        1.59 -     1.71: 0
        1.71 -     1.84: 33
  Bond restraints: 3255
  Sorted by residual:
  bond pdb=" N   ASP C 441 "
       pdb=" CA  ASP C 441 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.033 1.15e-02 7.56e+03 8.46e+00
  bond pdb=" N   MET C 443 "
       pdb=" CA  MET C 443 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.030 1.23e-02 6.61e+03 6.10e+00
  bond pdb=" N   ARG C 442 "
       pdb=" CA  ARG C 442 "
    ideal  model  delta    sigma   weight residual
    1.455  1.485 -0.030 1.21e-02 6.83e+03 6.07e+00
  bond pdb=" N   ARG C 440 "
       pdb=" CA  ARG C 440 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.030 1.41e-02 5.03e+03 4.41e+00
  bond pdb=" CA  PRO C 470 "
       pdb=" C   PRO C 470 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.029 1.42e-02 4.96e+03 4.12e+00
  ... (remaining 3250 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 4161
        1.49 -     2.98: 227
        2.98 -     4.47: 41
        4.47 -     5.96: 6
        5.96 -     7.45: 6
  Bond angle restraints: 4441
  Sorted by residual:
  angle pdb=" C   ARG C 472 "
        pdb=" CA  ARG C 472 "
        pdb=" CB  ARG C 472 "
      ideal   model   delta    sigma   weight residual
     110.37  103.10    7.27 1.54e+00 4.22e-01 2.23e+01
  angle pdb=" C   TYR A 206 "
        pdb=" CA  TYR A 206 "
        pdb=" CB  TYR A 206 "
      ideal   model   delta    sigma   weight residual
     110.79  104.73    6.06 1.66e+00 3.63e-01 1.33e+01
  angle pdb=" N   TYR A 206 "
        pdb=" CA  TYR A 206 "
        pdb=" C   TYR A 206 "
      ideal   model   delta    sigma   weight residual
     111.28  114.85   -3.57 1.09e+00 8.42e-01 1.07e+01
  angle pdb=" C   VAL A 271 "
        pdb=" N   ARG A 272 "
        pdb=" CA  ARG A 272 "
      ideal   model   delta    sigma   weight residual
     120.29  115.66    4.63 1.42e+00 4.96e-01 1.07e+01
  angle pdb=" C   THR A 274 "
        pdb=" N   VAL A 275 "
        pdb=" CA  VAL A 275 "
      ideal   model   delta    sigma   weight residual
     122.66  119.78    2.88 9.70e-01 1.06e+00 8.81e+00
  ... (remaining 4436 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.06: 1657
       13.06 -    26.12: 138
       26.12 -    39.18: 56
       39.18 -    52.24: 10
       52.24 -    65.30: 4
  Dihedral angle restraints: 1865
    sinusoidal: 656
      harmonic: 1209
  Sorted by residual:
  dihedral pdb=" CB  CYS A 302 "
           pdb=" SG  CYS A 302 "
           pdb=" SG  CYS A 377 "
           pdb=" CB  CYS A 377 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   27.70   65.30     1      1.00e+01 1.00e-02 5.59e+01
  dihedral pdb=" CA  ASP A 423 "
           pdb=" C   ASP A 423 "
           pdb=" N   GLY A 424 "
           pdb=" CA  GLY A 424 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.42  -19.58     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  PRO C 470 "
           pdb=" C   PRO C 470 "
           pdb=" N   GLU C 471 "
           pdb=" CA  GLU C 471 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.90  -19.10     0      5.00e+00 4.00e-02 1.46e+01
  ... (remaining 1862 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 406
       0.054 -    0.108: 93
       0.108 -    0.162: 19
       0.162 -    0.216: 2
       0.216 -    0.271: 1
  Chirality restraints: 521
  Sorted by residual:
  chirality pdb=" CA  ASP A 207 "
            pdb=" N   ASP A 207 "
            pdb=" C   ASP A 207 "
            pdb=" CB  ASP A 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" CA  TRP A 319 "
            pdb=" N   TRP A 319 "
            pdb=" C   TRP A 319 "
            pdb=" CB  TRP A 319 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.18 2.00e-01 2.50e+01 7.66e-01
  chirality pdb=" CA  TYR A 378 "
            pdb=" N   TYR A 378 "
            pdb=" C   TYR A 378 "
            pdb=" CB  TYR A 378 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.76e-01
  ... (remaining 518 not shown)

  Planarity restraints: 535
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 259 "   -0.012 2.00e-02 2.50e+03   2.33e-02 5.43e+00
        pdb=" C   SER A 259 "    0.040 2.00e-02 2.50e+03
        pdb=" O   SER A 259 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   MET A 260 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 260 "   -0.010 2.00e-02 2.50e+03   2.10e-02 4.39e+00
        pdb=" C   MET A 260 "    0.036 2.00e-02 2.50e+03
        pdb=" O   MET A 260 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   CYS A 261 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 222 "   -0.017 2.00e-02 2.50e+03   1.11e-02 3.07e+00
        pdb=" CG  TRP A 222 "    0.028 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 222 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 222 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 222 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 222 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 222 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 222 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 222 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 222 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 532 not shown)

  Histogram of nonbonded interaction distances:
        1.74 -     2.37: 7
        2.37 -     3.00: 1852
        3.00 -     3.64: 4590
        3.64 -     4.27: 6467
        4.27 -     4.90: 10774
  Nonbonded interactions: 23690
  Sorted by model distance:
  nonbonded pdb=" CG1 VAL C 426 "
            pdb=" OH  TYR C 478 "
     model   vdw
     1.739 3.460
  nonbonded pdb=" O   THR A 237 "
            pdb=" OG1 THR A 240 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OD2 ASP A 371 "
            pdb=" OG1 THR A 374 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OG  SER C 498 "
            pdb=" OE1 GLN C 500 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OE1 GLU C 471 "
            pdb=" NH2 ARG C 473 "
     model   vdw
     2.294 3.120
  ... (remaining 23685 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:             0.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.800
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7034
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      :  0.007   0.061   3257  Z= 0.336
  Angle     :  0.811   7.452   4445  Z= 0.487
  Chirality :  0.050   0.271    521
  Planarity :  0.004   0.034    535
  Dihedral  : 11.972  63.055   1079
  Min Nonbonded Distance : 1.739

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  1.86 %
    Favored  : 97.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.39), residues: 407
  helix:  0.47 (0.30), residues: 251
  sheet: -2.12 (1.74), residues: 10
  loop : -1.81 (0.47), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP A 222 
 HIS   0.004   0.001   HIS A 348 
 PHE   0.022   0.002   PHE A 312 
 TYR   0.022   0.003   TYR A 378 
 ARG   0.001   0.000   ARG A 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14711 (  204)
  hydrogen bonds       : angle       6.55541 (  603)
  SS BOND              : bond        0.01080 (    2)
  SS BOND              : angle       3.48586 (    4)
  covalent geometry    : bond        0.00728 ( 3255)
  covalent geometry    : angle       0.80423 ( 4441)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 ASN cc_start: 0.7282 (t0) cc_final: 0.6945 (t0)
REVERT: A  366 ARG cc_start: 0.6590 (mmt-90) cc_final: 0.6318 (mmt-90)
REVERT: A  479 LEU cc_start: 0.7769 (tp) cc_final: 0.7545 (tp)
REVERT: C  500 GLN cc_start: 0.7293 (mp10) cc_final: 0.6909 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 75
  average time/residue: 0.1509
  time to fit residues: 13.7273
Evaluate side-chains
  71 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.0870
   chunk 31 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:    0.1980
   chunk 19 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    7.9990
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
A 381 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.158038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.132255 restraints weight = 4867.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 2.28
r_work: 0.3544 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7213
moved from start:          0.1315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   3257  Z= 0.174
  Angle     :  0.605   8.928   4445  Z= 0.315
  Chirality :  0.042   0.194    521
  Planarity :  0.004   0.033    535
  Dihedral  :  4.297  18.636    440
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  9.32 %
    Favored  : 89.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.40), residues: 407
  helix:  1.04 (0.31), residues: 253
  sheet: -2.74 (1.59), residues: 12
  loop : -1.75 (0.47), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 222 
 HIS   0.004   0.001   HIS A 502 
 PHE   0.017   0.001   PHE A 312 
 TYR   0.017   0.002   TYR C 478 
 ARG   0.001   0.000   ARG C 442 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07346 (  204)
  hydrogen bonds       : angle       4.82639 (  603)
  SS BOND              : bond        0.00440 (    2)
  SS BOND              : angle       1.93884 (    4)
  covalent geometry    : bond        0.00374 ( 3255)
  covalent geometry    : angle       0.60253 ( 4441)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A  260 MET cc_start: 0.7799 (ttm) cc_final: 0.7477 (ttm)
REVERT: A  263 ASN cc_start: 0.7518 (t0) cc_final: 0.7247 (t0)
REVERT: A  479 LEU cc_start: 0.7800 (tp) cc_final: 0.7570 (tp)
REVERT: C  445 LEU cc_start: 0.8408 (mt) cc_final: 0.8178 (mp)
REVERT: C  500 GLN cc_start: 0.7644 (mp10) cc_final: 0.7306 (mp10)
  outliers start: 4
  outliers final: 3
  residues processed: 65
  average time/residue: 0.1138
  time to fit residues: 9.5057
Evaluate side-chains
  67 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain C residue  426 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 23 optimal weight:    0.0870
   chunk 5 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 27 optimal weight:    0.0070
   chunk 31 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.5976

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

Flipped N/Q/H residues before XYZ refinement:
A 381 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.154639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.124831 restraints weight = 4851.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 2.55
r_work: 0.3473 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7247
moved from start:          0.1609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   3257  Z= 0.200
  Angle     :  0.588   7.311   4445  Z= 0.311
  Chirality :  0.042   0.152    521
  Planarity :  0.004   0.037    535
  Dihedral  :  4.156  17.276    440
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 12.42 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.40), residues: 407
  helix:  1.07 (0.30), residues: 255
  sheet: -2.99 (1.52), residues: 12
  loop : -1.71 (0.49), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 319 
 HIS   0.004   0.001   HIS A 348 
 PHE   0.018   0.002   PHE A 312 
 TYR   0.017   0.002   TYR A 444 
 ARG   0.002   0.000   ARG A 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07284 (  204)
  hydrogen bonds       : angle       4.59518 (  603)
  SS BOND              : bond        0.00444 (    2)
  SS BOND              : angle       1.70208 (    4)
  covalent geometry    : bond        0.00451 ( 3255)
  covalent geometry    : angle       0.58609 ( 4441)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A  260 MET cc_start: 0.8018 (ttm) cc_final: 0.7675 (ttm)
REVERT: A  263 ASN cc_start: 0.7567 (t0) cc_final: 0.7298 (t0)
REVERT: A  444 TYR cc_start: 0.8483 (t80) cc_final: 0.7931 (t80)
REVERT: A  480 LYS cc_start: 0.7952 (ttmm) cc_final: 0.7734 (ttmt)
REVERT: C  500 GLN cc_start: 0.7675 (mp10) cc_final: 0.7443 (mp10)
  outliers start: 7
  outliers final: 6
  residues processed: 68
  average time/residue: 0.1289
  time to fit residues: 10.9774
Evaluate side-chains
  70 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain C residue  426 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 8 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 381 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.153057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.123084 restraints weight = 4943.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 2.52
r_work: 0.3397 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   3257  Z= 0.256
  Angle     :  0.629   7.102   4445  Z= 0.333
  Chirality :  0.044   0.162    521
  Planarity :  0.004   0.044    535
  Dihedral  :  4.258  18.767    440
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 15.22 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.40), residues: 407
  helix:  0.97 (0.30), residues: 254
  sheet: -3.02 (1.51), residues: 12
  loop : -1.73 (0.49), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 319 
 HIS   0.007   0.002   HIS A 348 
 PHE   0.020   0.002   PHE A 312 
 TYR   0.017   0.002   TYR A 378 
 ARG   0.004   0.001   ARG A 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07984 (  204)
  hydrogen bonds       : angle       4.65779 (  603)
  SS BOND              : bond        0.00438 (    2)
  SS BOND              : angle       1.58114 (    4)
  covalent geometry    : bond        0.00594 ( 3255)
  covalent geometry    : angle       0.62790 ( 4441)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
REVERT: A  263 ASN cc_start: 0.7611 (t0) cc_final: 0.7344 (t0)
REVERT: A  444 TYR cc_start: 0.8467 (t80) cc_final: 0.8063 (t80)
REVERT: C  500 GLN cc_start: 0.7652 (mp10) cc_final: 0.7261 (mp10)
  outliers start: 9
  outliers final: 8
  residues processed: 74
  average time/residue: 0.1431
  time to fit residues: 13.1866
Evaluate side-chains
  78 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain C residue  445 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 25 optimal weight:    0.3980
   chunk 32 optimal weight:    0.5980
   chunk 12 optimal weight:    0.1980
   chunk 38 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0870
   chunk 13 optimal weight:    0.1980
   chunk 16 optimal weight:    0.2980
   chunk 2 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.2358

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

Flipped N/Q/H residues before XYZ refinement:
A 381 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.157606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.128071 restraints weight = 4899.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 2.56
r_work: 0.3542 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7194
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3257  Z= 0.132
  Angle     :  0.545   6.748   4445  Z= 0.280
  Chirality :  0.039   0.135    521
  Planarity :  0.004   0.036    535
  Dihedral  :  3.843  16.433    440
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 18.01 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.41), residues: 407
  helix:  1.59 (0.31), residues: 254
  sheet: -2.99 (1.55), residues: 12
  loop : -1.69 (0.47), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 222 
 HIS   0.002   0.001   HIS A 502 
 PHE   0.015   0.001   PHE A 312 
 TYR   0.009   0.001   TYR A 265 
 ARG   0.003   0.000   ARG A 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05803 (  204)
  hydrogen bonds       : angle       4.11897 (  603)
  SS BOND              : bond        0.00200 (    2)
  SS BOND              : angle       0.72006 (    4)
  covalent geometry    : bond        0.00274 ( 3255)
  covalent geometry    : angle       0.54505 ( 4441)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: A  260 MET cc_start: 0.7839 (ttm) cc_final: 0.7537 (ttm)
REVERT: A  263 ASN cc_start: 0.7554 (t0) cc_final: 0.7305 (t0)
REVERT: A  272 ARG cc_start: 0.7975 (tmm-80) cc_final: 0.7262 (tmm-80)
REVERT: A  434 MET cc_start: 0.6592 (ptp) cc_final: 0.6285 (mtm)
REVERT: A  444 TYR cc_start: 0.8428 (t80) cc_final: 0.7788 (t80)
REVERT: A  462 TRP cc_start: 0.7968 (t-100) cc_final: 0.7722 (t-100)
REVERT: C  463 TYR cc_start: 0.6988 (t80) cc_final: 0.6577 (t80)
REVERT: C  500 GLN cc_start: 0.7679 (mp10) cc_final: 0.7338 (mp10)
  outliers start: 5
  outliers final: 4
  residues processed: 72
  average time/residue: 0.1547
  time to fit residues: 13.8096
Evaluate side-chains
  74 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  437 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 37 optimal weight:    4.9990
   chunk 20 optimal weight:    0.0030
   chunk 11 optimal weight:    0.3980
   chunk 7 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 10 optimal weight:    0.4980
   overall best weight:    0.4390

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.156107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.125972 restraints weight = 5045.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 2.58
r_work: 0.3499 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3257  Z= 0.161
  Angle     :  0.560   7.843   4445  Z= 0.286
  Chirality :  0.040   0.178    521
  Planarity :  0.004   0.037    535
  Dihedral  :  3.804  15.721    440
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 18.01 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.41), residues: 407
  helix:  1.62 (0.32), residues: 255
  sheet: -3.02 (1.55), residues: 12
  loop : -1.61 (0.49), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 222 
 HIS   0.004   0.001   HIS A 337 
 PHE   0.018   0.001   PHE A 312 
 TYR   0.009   0.001   TYR A 265 
 ARG   0.003   0.000   ARG A 272 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06254 (  204)
  hydrogen bonds       : angle       4.16919 (  603)
  SS BOND              : bond        0.00269 (    2)
  SS BOND              : angle       1.00067 (    4)
  covalent geometry    : bond        0.00360 ( 3255)
  covalent geometry    : angle       0.55966 ( 4441)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
REVERT: A  260 MET cc_start: 0.7927 (ttm) cc_final: 0.7606 (ttm)
REVERT: A  263 ASN cc_start: 0.7621 (t0) cc_final: 0.7377 (t0)
REVERT: A  272 ARG cc_start: 0.8030 (tmm-80) cc_final: 0.7340 (tmm-80)
REVERT: A  358 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7926 (mtmm)
REVERT: A  415 LYS cc_start: 0.7197 (ttmm) cc_final: 0.6997 (mtpt)
REVERT: A  434 MET cc_start: 0.6565 (ptp) cc_final: 0.6270 (mtm)
REVERT: A  444 TYR cc_start: 0.8433 (t80) cc_final: 0.7817 (t80)
REVERT: A  462 TRP cc_start: 0.8005 (t-100) cc_final: 0.7713 (t-100)
REVERT: C  500 GLN cc_start: 0.7688 (mp10) cc_final: 0.7343 (mp10)
  outliers start: 10
  outliers final: 6
  residues processed: 74
  average time/residue: 0.1519
  time to fit residues: 13.5805
Evaluate side-chains
  78 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  358 LYS
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain C residue  445 LEU
Chi-restraints excluded: chain C residue  505 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 21 optimal weight:    0.3980
   chunk 32 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0870
   chunk 9 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.6158

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.155278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.125406 restraints weight = 4894.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 2.52
r_work: 0.3487 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
moved from start:          0.2279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   3257  Z= 0.200
  Angle     :  0.571   7.013   4445  Z= 0.298
  Chirality :  0.041   0.154    521
  Planarity :  0.004   0.042    535
  Dihedral  :  3.888  17.518    440
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 17.08 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.41), residues: 407
  helix:  1.48 (0.31), residues: 254
  sheet: -3.06 (1.54), residues: 12
  loop : -1.59 (0.49), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 222 
 HIS   0.005   0.001   HIS A 337 
 PHE   0.018   0.002   PHE A 312 
 TYR   0.010   0.002   TYR A 378 
 ARG   0.003   0.000   ARG A 272 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06864 (  204)
  hydrogen bonds       : angle       4.27896 (  603)
  SS BOND              : bond        0.00336 (    2)
  SS BOND              : angle       1.15122 (    4)
  covalent geometry    : bond        0.00459 ( 3255)
  covalent geometry    : angle       0.56989 ( 4441)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
REVERT: A  260 MET cc_start: 0.7997 (ttm) cc_final: 0.7664 (ttm)
REVERT: A  263 ASN cc_start: 0.7665 (t0) cc_final: 0.7407 (t0)
REVERT: A  358 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7959 (mtmm)
REVERT: A  434 MET cc_start: 0.6553 (ptp) cc_final: 0.6299 (mtm)
REVERT: A  444 TYR cc_start: 0.8424 (t80) cc_final: 0.7806 (t80)
REVERT: C  500 GLN cc_start: 0.7693 (mp10) cc_final: 0.7380 (mp10)
  outliers start: 11
  outliers final: 8
  residues processed: 75
  average time/residue: 0.1482
  time to fit residues: 13.6400
Evaluate side-chains
  78 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  358 LYS
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain C residue  445 LEU
Chi-restraints excluded: chain C residue  505 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 15 optimal weight:    0.0000
   chunk 24 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 3 optimal weight:    0.3980
   chunk 2 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.4984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.155958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.126173 restraints weight = 4929.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 2.55
r_work: 0.3479 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3257  Z= 0.173
  Angle     :  0.569   7.748   4445  Z= 0.294
  Chirality :  0.040   0.145    521
  Planarity :  0.004   0.040    535
  Dihedral  :  3.852  17.174    440
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 18.32 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.41), residues: 407
  helix:  1.49 (0.31), residues: 254
  sheet: -3.17 (1.51), residues: 12
  loop : -1.52 (0.50), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 222 
 HIS   0.004   0.001   HIS A 337 
 PHE   0.017   0.001   PHE A 312 
 TYR   0.010   0.001   TYR A 265 
 ARG   0.003   0.000   ARG A 272 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06551 (  204)
  hydrogen bonds       : angle       4.23812 (  603)
  SS BOND              : bond        0.00291 (    2)
  SS BOND              : angle       1.00857 (    4)
  covalent geometry    : bond        0.00389 ( 3255)
  covalent geometry    : angle       0.56854 ( 4441)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 MET cc_start: 0.7967 (ttm) cc_final: 0.7645 (ttm)
REVERT: A  263 ASN cc_start: 0.7659 (t0) cc_final: 0.7397 (t0)
REVERT: A  358 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7953 (mtmm)
REVERT: A  434 MET cc_start: 0.6503 (ptp) cc_final: 0.6262 (mtm)
REVERT: A  462 TRP cc_start: 0.8054 (t-100) cc_final: 0.7747 (t-100)
REVERT: C  500 GLN cc_start: 0.7676 (mp10) cc_final: 0.7377 (mp10)
  outliers start: 10
  outliers final: 9
  residues processed: 71
  average time/residue: 0.1556
  time to fit residues: 13.6371
Evaluate side-chains
  77 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  358 LYS
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain C residue  445 LEU
Chi-restraints excluded: chain C residue  505 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 12 optimal weight:    0.0980
   chunk 17 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0870
   chunk 18 optimal weight:    0.3980
   chunk 11 optimal weight:    0.2980
   chunk 10 optimal weight:    0.0010
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.1764

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.159159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.129555 restraints weight = 4961.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 2.55
r_work: 0.3541 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   3257  Z= 0.119
  Angle     :  0.528   7.586   4445  Z= 0.270
  Chirality :  0.039   0.130    521
  Planarity :  0.003   0.036    535
  Dihedral  :  3.665  14.720    440
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 19.25 %
    Favored  : 78.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.42), residues: 407
  helix:  1.85 (0.32), residues: 254
  sheet: -3.23 (1.49), residues: 12
  loop : -1.50 (0.49), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 222 
 HIS   0.002   0.001   HIS A 337 
 PHE   0.016   0.001   PHE A 312 
 TYR   0.008   0.001   TYR A 265 
 ARG   0.001   0.000   ARG C 442 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05180 (  204)
  hydrogen bonds       : angle       3.95266 (  603)
  SS BOND              : bond        0.00141 (    2)
  SS BOND              : angle       0.48718 (    4)
  covalent geometry    : bond        0.00237 ( 3255)
  covalent geometry    : angle       0.52792 ( 4441)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: A  250 TYR cc_start: 0.7210 (m-80) cc_final: 0.6101 (m-80)
REVERT: A  260 MET cc_start: 0.7946 (ttm) cc_final: 0.7648 (ttm)
REVERT: A  263 ASN cc_start: 0.7643 (t0) cc_final: 0.7390 (t0)
REVERT: A  358 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7932 (mtmm)
REVERT: A  415 LYS cc_start: 0.7171 (ttmm) cc_final: 0.6832 (mtpt)
REVERT: A  441 SER cc_start: 0.8281 (p) cc_final: 0.7984 (p)
REVERT: C  463 TYR cc_start: 0.6983 (t80) cc_final: 0.6525 (t80)
  outliers start: 8
  outliers final: 6
  residues processed: 81
  average time/residue: 0.1359
  time to fit residues: 13.5670
Evaluate side-chains
  83 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  358 LYS
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain C residue  445 LEU
Chi-restraints excluded: chain C residue  505 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 16 optimal weight:    0.0040
   chunk 27 optimal weight:    0.7980
   chunk 40 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0170
   chunk 14 optimal weight:    0.5980
   chunk 3 optimal weight:    0.4980
   chunk 10 optimal weight:    0.2980
   chunk 18 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.2630

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.159006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.128809 restraints weight = 4899.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3669 rms_B_bonded: 2.59
r_work: 0.3545 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.2947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3257  Z= 0.132
  Angle     :  0.592  11.283   4445  Z= 0.294
  Chirality :  0.040   0.170    521
  Planarity :  0.003   0.035    535
  Dihedral  :  3.654  14.280    440
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 22.36 %
    Favored  : 75.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.41), residues: 407
  helix:  1.72 (0.32), residues: 254
  sheet: -3.25 (1.49), residues: 12
  loop : -1.42 (0.49), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 222 
 HIS   0.003   0.001   HIS A 337 
 PHE   0.017   0.001   PHE A 312 
 TYR   0.009   0.001   TYR A 265 
 ARG   0.002   0.000   ARG A 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05481 (  204)
  hydrogen bonds       : angle       4.00558 (  603)
  SS BOND              : bond        0.00171 (    2)
  SS BOND              : angle       0.66809 (    4)
  covalent geometry    : bond        0.00280 ( 3255)
  covalent geometry    : angle       0.59210 ( 4441)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
REVERT: A  250 TYR cc_start: 0.7242 (m-80) cc_final: 0.5986 (m-80)
REVERT: A  263 ASN cc_start: 0.7670 (t0) cc_final: 0.7425 (t0)
REVERT: A  358 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7902 (mtmm)
REVERT: A  415 LYS cc_start: 0.7019 (ttmm) cc_final: 0.6816 (mtpt)
REVERT: A  441 SER cc_start: 0.8278 (p) cc_final: 0.8003 (p)
REVERT: C  463 TYR cc_start: 0.6944 (t80) cc_final: 0.6492 (t80)
  outliers start: 7
  outliers final: 5
  residues processed: 74
  average time/residue: 0.1577
  time to fit residues: 14.4396
Evaluate side-chains
  78 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  358 LYS
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain C residue  445 LEU
Chi-restraints excluded: chain C residue  505 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0570
   chunk 26 optimal weight:    0.7980
   chunk 3 optimal weight:    0.1980
   chunk 17 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.5098

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.156143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.125505 restraints weight = 4911.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 2.57
r_work: 0.3489 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7247
moved from start:          0.2813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3257  Z= 0.175
  Angle     :  0.621  10.876   4445  Z= 0.311
  Chirality :  0.041   0.150    521
  Planarity :  0.004   0.038    535
  Dihedral  :  3.780  16.269    440
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 22.67 %
    Favored  : 75.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.41), residues: 407
  helix:  1.52 (0.32), residues: 255
  sheet: -3.28 (1.49), residues: 12
  loop : -1.53 (0.50), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 222 
 HIS   0.004   0.001   HIS A 337 
 PHE   0.017   0.001   PHE A 312 
 TYR   0.010   0.001   TYR A 265 
 ARG   0.002   0.000   ARG A 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06401 (  204)
  hydrogen bonds       : angle       4.15131 (  603)
  SS BOND              : bond        0.00294 (    2)
  SS BOND              : angle       1.02080 (    4)
  covalent geometry    : bond        0.00396 ( 3255)
  covalent geometry    : angle       0.62087 ( 4441)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1853.57 seconds
wall clock time: 32 minutes 57.06 seconds (1977.06 seconds total)