Starting phenix.real_space_refine
on Fri May  9 19:14:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qw4_18680/05_2025/8qw4_18680.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qw4_18680/05_2025/8qw4_18680.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qw4_18680/05_2025/8qw4_18680.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qw4_18680/05_2025/8qw4_18680.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qw4_18680/05_2025/8qw4_18680.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qw4_18680/05_2025/8qw4_18680.cif"
  }
  resolution = 2.9
  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=   0.019
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      27      5.16       5
     C    2286      2.51       5
     N     564      2.21       5
     O     602      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3479
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 320, 2591
          Classifications: {'peptide': 320}
          Link IDs: {'PTRANS': 13, 'TRANS': 306}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 888
          Classifications: {'peptide': 114}
          Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 111}
          Chain breaks: 1
  Time building chain proxies: 4.80, per 1000 atoms: 1.38
  Number of scatterers: 3479
  At special positions: 0
  Unit cell: (93.072, 57.339, 101.382, 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      27     16.00
     O     602      8.00
     N     564      7.00
     C    2286      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 165 " - pdb=" SG  CYS A 185 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 189 " - pdb=" SG  CYS A 264 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 286 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  25 " - pdb=" SG  CYS B  98 " distance=2.02

  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: 0.80
  Conformation dependent library (CDL) restraints added in 368.6 milliseconds
  

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  808

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 4 sheets defined
      52.5% alpha, 8.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 195 through 225
      removed outlier: 3.885A  pdb=" N   LEU A 199 " --> pdb=" O   ARG A 195 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   TYR A 204 " --> pdb=" O   SER A 200 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   GLY A 207 " --> pdb=" O   ARG A 203 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   ILE A 212 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   THR A 220 " --> pdb=" O   ALA A 216 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   PHE A 221 " --> pdb=" O   THR A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 253
      removed outlier: 3.963A  pdb=" N   PHE A 240 " --> pdb=" O   ARG A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 256
      No H-bonds generated for 'chain 'A' and resid 254 through 256'
    Processing helix  chain 'A' and resid 283 through 313
      removed outlier: 3.615A  pdb=" N   THR A 287 " --> pdb=" O   ASN A 283 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   MET A 288 " --> pdb=" O   LYS A 284 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   LEU A 289 " --> pdb=" O   ALA A 285 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   PHE A 290 " --> pdb=" O   CYS A 286 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   MET A 291 " --> pdb=" O   THR A 287 " (cutoff:3.500A)
      removed outlier: 5.276A  pdb=" N   ILE A 292 " --> pdb=" O   MET A 288 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   PHE A 295 " --> pdb=" O   MET A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 326
    Processing helix  chain 'A' and resid 327 through 345
      Proline residue:  A 339  - end of helix
    Processing helix  chain 'A' and resid 367 through 375
      removed outlier: 3.625A  pdb=" N   LEU A 371 " --> pdb=" O   ASP A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 402
      removed outlier: 4.147A  pdb=" N   SER A 396 " --> pdb=" O   ALA A 392 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ARG A 399 " --> pdb=" O   ILE A 395 " (cutoff:3.500A)
      removed outlier: 4.871A  pdb=" N   VAL A 400 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ARG A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   ILE A 402 " --> pdb=" O   ASN A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 411
    Processing helix  chain 'A' and resid 413 through 443
      removed outlier: 4.077A  pdb=" N   PHE A 417 " --> pdb=" O   LYS A 413 " (cutoff:3.500A)
      Proline residue:  A 431  - end of helix
    Processing helix  chain 'A' and resid 445 through 452
      removed outlier: 3.647A  pdb=" N   TRP A 449 " --> pdb=" O   TYR A 445 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLU A 450 " --> pdb=" O   ARG A 446 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   THR A 451 " --> pdb=" O   GLY A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 457
    Processing helix  chain 'A' and resid 474 through 479
      removed outlier: 3.533A  pdb=" N   LEU A 479 " --> pdb=" O   PRO A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 489
      removed outlier: 3.598A  pdb=" N   TYR A 484 " --> pdb=" O   PHE A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 493
      Proline residue:  A 493  - end of helix
      No H-bonds generated for 'chain 'A' and resid 490 through 493'
    Processing helix  chain 'A' and resid 494 through 499
    Processing helix  chain 'B' and resid 89 through 93
    Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178
      removed outlier: 6.357A  pdb=" N   TYR A 177 " --> pdb=" O   CYS A 185 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 27
      removed outlier: 4.382A  pdb=" N   ASP B  79 " --> pdb=" O   ALA B  27 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 62
      removed outlier: 6.821A  pdb=" N   TRP B  39 " --> pdb=" O   VAL B  51 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   ASP B  53 " --> pdb=" O   MET B  37 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   MET B  37 " --> pdb=" O   ASP B  53 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   VAL B  36 " --> pdb=" O   GLU B 101 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 94 through 95

    156 hydrogen bonds defined for protein.
    438 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: 0.81

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1034
        1.34 -     1.46: 921
        1.46 -     1.59: 1564
        1.59 -     1.71: 0
        1.71 -     1.83: 41
  Bond restraints: 3560
  Sorted by residual:
  bond pdb=" N   GLU A 407 "
       pdb=" CA  GLU A 407 "
    ideal  model  delta    sigma   weight residual
    1.460  1.486 -0.026 1.50e-02 4.44e+03 2.99e+00
  bond pdb=" C   ASP A 476 "
       pdb=" N   LEU A 477 "
    ideal  model  delta    sigma   weight residual
    1.331  1.307  0.024 1.40e-02 5.10e+03 2.97e+00
  bond pdb=" C   LEU A 406 "
       pdb=" N   GLU A 407 "
    ideal  model  delta    sigma   weight residual
    1.330  1.351 -0.021 1.28e-02 6.10e+03 2.77e+00
  bond pdb=" CB  THR A 276 "
       pdb=" CG2 THR A 276 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.63e+00
  bond pdb=" CB  TYR A 177 "
       pdb=" CG  TYR A 177 "
    ideal  model  delta    sigma   weight residual
    1.512  1.477  0.035 2.20e-02 2.07e+03 2.48e+00
  ... (remaining 3555 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 4614
        2.38 -     4.76: 169
        4.76 -     7.14: 31
        7.14 -     9.52: 5
        9.52 -    11.91: 3
  Bond angle restraints: 4822
  Sorted by residual:
  angle pdb=" C   GLU A 235 "
        pdb=" N   ARG A 236 "
        pdb=" CA  ARG A 236 "
      ideal   model   delta    sigma   weight residual
     120.09  125.89   -5.80 1.25e+00 6.40e-01 2.15e+01
  angle pdb=" N   ARG A 459 "
        pdb=" CA  ARG A 459 "
        pdb=" C   ARG A 459 "
      ideal   model   delta    sigma   weight residual
     110.80  101.02    9.78 2.13e+00 2.20e-01 2.11e+01
  angle pdb=" N   GLY A 354 "
        pdb=" CA  GLY A 354 "
        pdb=" C   GLY A 354 "
      ideal   model   delta    sigma   weight residual
     112.13  118.02   -5.89 1.34e+00 5.57e-01 1.93e+01
  angle pdb=" C   ALA B  43 "
        pdb=" N   PRO B  44 "
        pdb=" CA  PRO B  44 "
      ideal   model   delta    sigma   weight residual
     127.00  136.73   -9.73 2.40e+00 1.74e-01 1.64e+01
  angle pdb=" C   CYS A 458 "
        pdb=" N   ARG A 459 "
        pdb=" CA  ARG A 459 "
      ideal   model   delta    sigma   weight residual
     121.54  129.22   -7.68 1.91e+00 2.74e-01 1.62e+01
  ... (remaining 4817 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.29: 1877
       16.29 -    32.57: 177
       32.57 -    48.86: 30
       48.86 -    65.14: 4
       65.14 -    81.43: 6
  Dihedral angle restraints: 2094
    sinusoidal: 837
      harmonic: 1257
  Sorted by residual:
  dihedral pdb=" CB  CYS A 189 "
           pdb=" SG  CYS A 189 "
           pdb=" SG  CYS A 264 "
           pdb=" CB  CYS A 264 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -157.10   71.10     1      1.00e+01 1.00e-02 6.49e+01
  dihedral pdb=" CA  TYR A 177 "
           pdb=" C   TYR A 177 "
           pdb=" N   SER A 178 "
           pdb=" CA  SER A 178 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.73  -34.27     0      5.00e+00 4.00e-02 4.70e+01
  dihedral pdb=" CA  SER A 178 "
           pdb=" C   SER A 178 "
           pdb=" N   PHE A 179 "
           pdb=" CA  PHE A 179 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.92  -33.08     0      5.00e+00 4.00e-02 4.38e+01
  ... (remaining 2091 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 361
       0.048 -    0.096: 136
       0.096 -    0.144: 34
       0.144 -    0.192: 17
       0.192 -    0.241: 2
  Chirality restraints: 550
  Sorted by residual:
  chirality pdb=" CA  VAL A 316 "
            pdb=" N   VAL A 316 "
            pdb=" C   VAL A 316 "
            pdb=" CB  VAL A 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.20    0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" CA  PRO B  90 "
            pdb=" N   PRO B  90 "
            pdb=" C   PRO B  90 "
            pdb=" CB  PRO B  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.51    0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" CA  PRO A 405 "
            pdb=" N   PRO A 405 "
            pdb=" C   PRO A 405 "
            pdb=" CB  PRO A 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 9.11e-01
  ... (remaining 547 not shown)

  Planarity restraints: 587
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 316 "   -0.077 5.00e-02 4.00e+02   1.16e-01 2.14e+01
        pdb=" N   PRO A 317 "    0.200 5.00e-02 4.00e+02
        pdb=" CA  PRO A 317 "   -0.060 5.00e-02 4.00e+02
        pdb=" CD  PRO A 317 "   -0.063 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 474 "    0.035 5.00e-02 4.00e+02   5.29e-02 4.47e+00
        pdb=" N   PRO A 475 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 475 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 475 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 428 "    0.010 2.00e-02 2.50e+03   1.41e-02 3.99e+00
        pdb=" CG  TYR A 428 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 428 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 428 "    0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 428 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 428 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 428 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 428 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 584 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 75
        2.65 -     3.21: 3457
        3.21 -     3.78: 5258
        3.78 -     4.34: 7053
        4.34 -     4.90: 11275
  Nonbonded interactions: 27118
  Sorted by model distance:
  nonbonded pdb=" O   GLN A 455 "
            pdb=" NH2 ARG A 459 "
     model   vdw
     2.091 3.120
  nonbonded pdb=" OH  TYR A 241 "
            pdb=" O   VAL A 490 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   ASN A 410 "
            pdb=" N   LYS A 413 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" O   ASP A 260 "
            pdb=" NH1 ARG A 261 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" O   THR A 217 "
            pdb=" OG1 THR A 220 "
     model   vdw
     2.300 3.040
  ... (remaining 27113 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:             9.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     14.710
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:10.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6284
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   0.057   3564  Z= 0.338
  Angle     :  1.104  11.906   4830  Z= 0.610
  Chirality :  0.058   0.241    550
  Planarity :  0.008   0.116    587
  Dihedral  : 13.197  81.429   1274
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 17.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.05 %
    Favored  : 85.95 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.00 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.25 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.49 %

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: -3.29 (0.39), residues: 420
  helix: -0.99 (0.37), residues: 189
  sheet: -1.69 (0.86), residues: 38
  loop : -3.62 (0.39), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 104 
 HIS   0.003   0.001   HIS A 282 
 PHE   0.020   0.003   PHE A 201 
 TYR   0.034   0.003   TYR A 428 
 ARG   0.009   0.001   ARG B  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16799 (  156)
  hydrogen bonds       : angle       6.60400 (  438)
  SS BOND              : bond        0.00704 (    4)
  SS BOND              : angle       3.02074 (    8)
  covalent geometry    : bond        0.00748 ( 3560)
  covalent geometry    : angle       1.09835 ( 4822)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 ARG cc_start: 0.6980 (tpt90) cc_final: 0.5436 (mtp180)
REVERT: A  336 TRP cc_start: 0.7890 (m100) cc_final: 0.7653 (m-10)
REVERT: A  349 MET cc_start: 0.4417 (mmt) cc_final: 0.3595 (ptt)
REVERT: A  442 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6685 (mp0)
REVERT: B   35 ASP cc_start: 0.7720 (m-30) cc_final: 0.7504 (m-30)
REVERT: B   55 THR cc_start: 0.7761 (p) cc_final: 0.7495 (m)
  outliers start: 1
  outliers final: 2
  residues processed: 119
  average time/residue: 0.8532
  time to fit residues: 105.3265
Evaluate side-chains
  66 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  279 GLN
Chi-restraints excluded: chain A residue  352 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 32 optimal weight:    0.2980
   chunk 18 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 13 optimal weight:    0.3980
   chunk 20 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 265 ASN
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 443 GLN ** 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 = 0.4510 r_free = 0.4510 target = 0.185062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.169331 restraints weight = 7913.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.4351 rms_B_bonded: 3.53
r_work: 0.4256 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.4256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6550
moved from start:          0.2981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   3564  Z= 0.189
  Angle     :  0.879   8.375   4830  Z= 0.449
  Chirality :  0.051   0.189    550
  Planarity :  0.007   0.069    587
  Dihedral  :  7.421  36.115    478
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.05 %
    Favored  : 90.95 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 17.94 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -2.85 (0.39), residues: 420
  helix: -0.77 (0.37), residues: 191
  sheet: -1.06 (0.85), residues: 38
  loop : -3.34 (0.40), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 449 
 HIS   0.001   0.001   HIS A 282 
 PHE   0.026   0.002   PHE B  32 
 TYR   0.018   0.002   TYR A 428 
 ARG   0.006   0.001   ARG B  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05006 (  156)
  hydrogen bonds       : angle       5.39730 (  438)
  SS BOND              : bond        0.00292 (    4)
  SS BOND              : angle       1.19809 (    8)
  covalent geometry    : bond        0.00437 ( 3560)
  covalent geometry    : angle       0.87880 ( 4822)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.360 
Fit side-chains
REVERT: A  193 TYR cc_start: 0.5710 (OUTLIER) cc_final: 0.5492 (m-80)
REVERT: A  203 ARG cc_start: 0.6718 (tpt90) cc_final: 0.5224 (mtp180)
REVERT: A  291 MET cc_start: 0.6459 (ptt) cc_final: 0.6157 (pmm)
REVERT: A  336 TRP cc_start: 0.8460 (m100) cc_final: 0.7686 (m-10)
REVERT: A  349 MET cc_start: 0.5041 (mmt) cc_final: 0.3570 (ptt)
REVERT: A  367 ASP cc_start: 0.7853 (t0) cc_final: 0.7554 (t0)
REVERT: A  415 VAL cc_start: 0.6072 (OUTLIER) cc_final: 0.4956 (t)
REVERT: A  433 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7814 (tm)
REVERT: A  445 TYR cc_start: 0.6772 (t80) cc_final: 0.6509 (t80)
REVERT: B   35 ASP cc_start: 0.8735 (m-30) cc_final: 0.8478 (m-30)
REVERT: B  109 TYR cc_start: 0.7766 (m-80) cc_final: 0.7356 (m-80)
  outliers start: 19
  outliers final: 7
  residues processed: 81
  average time/residue: 0.9405
  time to fit residues: 79.0147
Evaluate side-chains
  75 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 TYR
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  213 CYS
Chi-restraints excluded: chain A residue  279 GLN
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  102 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 8 optimal weight:    0.0570
   chunk 1 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 32 optimal weight:    0.3980
   chunk 14 optimal weight:    0.0770
   chunk 13 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0030
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.2266

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.187327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.172088 restraints weight = 8110.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.4390 rms_B_bonded: 3.55
r_work: 0.4297 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.4297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6514
moved from start:          0.3689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3564  Z= 0.152
  Angle     :  0.789   8.333   4830  Z= 0.401
  Chirality :  0.048   0.278    550
  Planarity :  0.006   0.059    587
  Dihedral  :  6.743  35.450    476
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.05 %
    Favored  : 90.95 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 22.96 %
    Favored  : 73.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -2.54 (0.40), residues: 420
  helix: -0.38 (0.38), residues: 189
  sheet: -1.07 (0.82), residues: 36
  loop : -3.25 (0.40), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 449 
 HIS   0.001   0.000   HIS A 332 
 PHE   0.020   0.002   PHE B  32 
 TYR   0.020   0.002   TYR A 428 
 ARG   0.005   0.001   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04425 (  156)
  hydrogen bonds       : angle       5.10665 (  438)
  SS BOND              : bond        0.00189 (    4)
  SS BOND              : angle       0.84704 (    8)
  covalent geometry    : bond        0.00337 ( 3560)
  covalent geometry    : angle       0.78878 ( 4822)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
REVERT: A  326 LYS cc_start: 0.9047 (mtmm) cc_final: 0.8825 (mtmm)
REVERT: A  336 TRP cc_start: 0.8320 (m100) cc_final: 0.7567 (m-10)
REVERT: A  349 MET cc_start: 0.4775 (mmt) cc_final: 0.3406 (ptt)
REVERT: A  367 ASP cc_start: 0.7671 (t0) cc_final: 0.7229 (t0)
REVERT: A  415 VAL cc_start: 0.5773 (OUTLIER) cc_final: 0.4559 (t)
REVERT: A  433 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7824 (tm)
REVERT: A  482 MET cc_start: 0.7558 (ppp) cc_final: 0.7328 (pp-130)
REVERT: B   35 ASP cc_start: 0.8821 (m-30) cc_final: 0.8523 (m-30)
REVERT: B  109 TYR cc_start: 0.7762 (m-80) cc_final: 0.7448 (m-80)
  outliers start: 15
  outliers final: 5
  residues processed: 84
  average time/residue: 0.7972
  time to fit residues: 69.9827
Evaluate side-chains
  72 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 TYR
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  279 GLN
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  102 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0870
   chunk 30 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.184528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.169077 restraints weight = 8057.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.4353 rms_B_bonded: 3.60
r_work: 0.4257 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.4257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6587
moved from start:          0.3910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3564  Z= 0.175
  Angle     :  0.811   9.513   4830  Z= 0.406
  Chirality :  0.048   0.172    550
  Planarity :  0.005   0.062    587
  Dihedral  :  6.687  34.109    476
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.29 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 25.07 %
    Favored  : 69.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -2.30 (0.41), residues: 420
  helix: -0.24 (0.38), residues: 189
  sheet: -0.88 (0.84), residues: 36
  loop : -3.07 (0.42), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 449 
 HIS   0.002   0.001   HIS A 282 
 PHE   0.015   0.002   PHE B  32 
 TYR   0.026   0.002   TYR A 428 
 ARG   0.005   0.000   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04357 (  156)
  hydrogen bonds       : angle       5.01176 (  438)
  SS BOND              : bond        0.00281 (    4)
  SS BOND              : angle       0.74116 (    8)
  covalent geometry    : bond        0.00407 ( 3560)
  covalent geometry    : angle       0.81125 ( 4822)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 ARG cc_start: 0.6695 (OUTLIER) cc_final: 0.5191 (tpt-90)
REVERT: A  291 MET cc_start: 0.6333 (ptt) cc_final: 0.5601 (pmm)
REVERT: A  336 TRP cc_start: 0.8360 (m100) cc_final: 0.7563 (m-10)
REVERT: A  349 MET cc_start: 0.4869 (mmt) cc_final: 0.3833 (ptt)
REVERT: A  415 VAL cc_start: 0.5995 (OUTLIER) cc_final: 0.4766 (t)
REVERT: A  433 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7823 (tm)
REVERT: A  445 TYR cc_start: 0.6595 (t80) cc_final: 0.6313 (t80)
REVERT: B   35 ASP cc_start: 0.8847 (m-30) cc_final: 0.8533 (m-30)
REVERT: B  109 TYR cc_start: 0.7808 (m-80) cc_final: 0.7457 (m-80)
  outliers start: 21
  outliers final: 7
  residues processed: 84
  average time/residue: 0.8712
  time to fit residues: 76.0873
Evaluate side-chains
  73 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  203 ARG
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  102 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 37 optimal weight:    0.3980
   chunk 4 optimal weight:    0.4980
   chunk 2 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 33 optimal weight:    0.3980
   chunk 8 optimal weight:    0.2980
   chunk 20 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0030
   chunk 39 optimal weight:    0.5980
   chunk 1 optimal weight:    0.4980
   overall best weight:    0.3190

-------------------------------------------------------------------------------
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 = 0.4530 r_free = 0.4530 target = 0.186442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.171127 restraints weight = 8109.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.4376 rms_B_bonded: 3.67
r_work: 0.4279 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.4279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6522
moved from start:          0.4305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3564  Z= 0.147
  Angle     :  0.810  10.458   4830  Z= 0.395
  Chirality :  0.046   0.180    550
  Planarity :  0.005   0.056    587
  Dihedral  :  6.183  27.685    473
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 27.97 %
    Favored  : 67.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -2.21 (0.41), residues: 420
  helix: -0.23 (0.39), residues: 190
  sheet: -0.63 (0.88), residues: 36
  loop : -3.00 (0.44), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 449 
 HIS   0.001   0.000   HIS A 282 
 PHE   0.025   0.002   PHE A 224 
 TYR   0.016   0.001   TYR A 204 
 ARG   0.005   0.000   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04167 (  156)
  hydrogen bonds       : angle       4.97185 (  438)
  SS BOND              : bond        0.00149 (    4)
  SS BOND              : angle       0.61128 (    8)
  covalent geometry    : bond        0.00338 ( 3560)
  covalent geometry    : angle       0.80995 ( 4822)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 ARG cc_start: 0.6670 (tpt90) cc_final: 0.5244 (tpt-90)
REVERT: A  250 LEU cc_start: 0.8117 (tt) cc_final: 0.7783 (tt)
REVERT: A  349 MET cc_start: 0.4763 (mmt) cc_final: 0.3489 (ptt)
REVERT: A  367 ASP cc_start: 0.7951 (t0) cc_final: 0.7723 (t0)
REVERT: A  415 VAL cc_start: 0.5903 (OUTLIER) cc_final: 0.4643 (t)
REVERT: A  433 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7835 (tm)
REVERT: A  445 TYR cc_start: 0.6510 (t80) cc_final: 0.6269 (t80)
REVERT: A  482 MET cc_start: 0.7550 (ppp) cc_final: 0.7018 (mtt)
REVERT: A  501 LYS cc_start: 0.8541 (tppp) cc_final: 0.8280 (mmmt)
REVERT: B   35 ASP cc_start: 0.8867 (m-30) cc_final: 0.8571 (m-30)
REVERT: B  103 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7899 (tp30)
REVERT: B  109 TYR cc_start: 0.7807 (m-80) cc_final: 0.7423 (m-80)
  outliers start: 19
  outliers final: 9
  residues processed: 82
  average time/residue: 0.8035
  time to fit residues: 68.7207
Evaluate side-chains
  75 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  102 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0050
   chunk 35 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0970
   chunk 40 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0020
   overall best weight:    0.3000

-------------------------------------------------------------------------------
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 = 0.4532 r_free = 0.4532 target = 0.186486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.171297 restraints weight = 8154.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.4374 rms_B_bonded: 3.67
r_work: 0.4280 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.4280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6531
moved from start:          0.4500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3564  Z= 0.146
  Angle     :  0.802  10.212   4830  Z= 0.388
  Chirality :  0.045   0.175    550
  Planarity :  0.005   0.058    587
  Dihedral  :  6.032  27.989    473
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 28.23 %
    Favored  : 67.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -2.10 (0.42), residues: 420
  helix: -0.13 (0.39), residues: 189
  sheet: -0.54 (0.89), residues: 36
  loop : -2.96 (0.44), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 449 
 HIS   0.001   0.000   HIS A 282 
 PHE   0.018   0.002   PHE A 253 
 TYR   0.025   0.002   TYR A 428 
 ARG   0.006   0.000   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04057 (  156)
  hydrogen bonds       : angle       4.90540 (  438)
  SS BOND              : bond        0.00160 (    4)
  SS BOND              : angle       0.56530 (    8)
  covalent geometry    : bond        0.00334 ( 3560)
  covalent geometry    : angle       0.80196 ( 4822)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.5298 (tpt-90)
REVERT: A  291 MET cc_start: 0.6015 (ptt) cc_final: 0.5287 (pmm)
REVERT: A  349 MET cc_start: 0.4644 (mmt) cc_final: 0.3250 (ptt)
REVERT: A  367 ASP cc_start: 0.7889 (t0) cc_final: 0.7602 (t0)
REVERT: A  415 VAL cc_start: 0.5955 (OUTLIER) cc_final: 0.4642 (t)
REVERT: A  433 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7827 (tm)
REVERT: A  445 TYR cc_start: 0.6548 (t80) cc_final: 0.6307 (t80)
REVERT: A  482 MET cc_start: 0.7597 (ppp) cc_final: 0.7062 (mtt)
REVERT: A  501 LYS cc_start: 0.8608 (tppp) cc_final: 0.8345 (mmmt)
REVERT: B   35 ASP cc_start: 0.8836 (m-30) cc_final: 0.8544 (m-30)
REVERT: B  103 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7959 (tp30)
REVERT: B  109 TYR cc_start: 0.7826 (m-80) cc_final: 0.7531 (m-80)
  outliers start: 17
  outliers final: 7
  residues processed: 82
  average time/residue: 0.8745
  time to fit residues: 74.5627
Evaluate side-chains
  72 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  203 ARG
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  108 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 33 optimal weight:    0.1980
   chunk 34 optimal weight:    1.9990
   chunk 5 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0570
   chunk 26 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.4098

-------------------------------------------------------------------------------
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 = 0.4528 r_free = 0.4528 target = 0.185968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.170688 restraints weight = 7944.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.4368 rms_B_bonded: 3.66
r_work: 0.4270 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.4270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6575
moved from start:          0.4630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3564  Z= 0.155
  Angle     :  0.830  10.812   4830  Z= 0.404
  Chirality :  0.046   0.173    550
  Planarity :  0.005   0.060    587
  Dihedral  :  6.010  27.403    473
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.57 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 29.02 %
    Favored  : 65.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -2.15 (0.41), residues: 420
  helix: -0.16 (0.39), residues: 189
  sheet: -0.55 (0.86), residues: 35
  loop : -2.99 (0.44), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 449 
 HIS   0.001   0.000   HIS A 282 
 PHE   0.014   0.002   PHE A 240 
 TYR   0.030   0.002   TYR A 428 
 ARG   0.006   0.000   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04011 (  156)
  hydrogen bonds       : angle       4.90900 (  438)
  SS BOND              : bond        0.00183 (    4)
  SS BOND              : angle       0.61740 (    8)
  covalent geometry    : bond        0.00366 ( 3560)
  covalent geometry    : angle       0.82995 ( 4822)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 65
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.5256 (tpt-90)
REVERT: A  291 MET cc_start: 0.5992 (ptt) cc_final: 0.5245 (pmm)
REVERT: A  349 MET cc_start: 0.4843 (mmt) cc_final: 0.3464 (ptt)
REVERT: A  367 ASP cc_start: 0.7848 (t0) cc_final: 0.7602 (t0)
REVERT: A  433 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7880 (tm)
REVERT: A  445 TYR cc_start: 0.6619 (t80) cc_final: 0.6368 (t80)
REVERT: A  482 MET cc_start: 0.7594 (ppp) cc_final: 0.7114 (mtt)
REVERT: A  501 LYS cc_start: 0.8591 (tppp) cc_final: 0.8343 (mmmt)
REVERT: B   35 ASP cc_start: 0.8819 (m-30) cc_final: 0.8528 (m-30)
REVERT: B  103 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8023 (tp30)
REVERT: B  109 TYR cc_start: 0.7824 (m-80) cc_final: 0.7514 (m-80)
  outliers start: 19
  outliers final: 11
  residues processed: 77
  average time/residue: 0.8649
  time to fit residues: 69.2717
Evaluate side-chains
  74 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  203 ARG
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  108 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 25 optimal weight:    0.1980
   chunk 35 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 22 optimal weight:    0.2980
   chunk 11 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0970
   chunk 29 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.3978

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.185454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.170309 restraints weight = 8027.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.4366 rms_B_bonded: 3.65
r_work: 0.4269 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.4269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6571
moved from start:          0.4801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3564  Z= 0.156
  Angle     :  0.859  11.583   4830  Z= 0.412
  Chirality :  0.047   0.182    550
  Planarity :  0.005   0.060    587
  Dihedral  :  5.894  27.493    473
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.57 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 29.29 %
    Favored  : 65.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -2.05 (0.42), residues: 420
  helix: -0.01 (0.40), residues: 189
  sheet: -0.60 (0.86), residues: 35
  loop : -2.99 (0.44), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 104 
 HIS   0.001   0.000   HIS A 282 
 PHE   0.011   0.002   PHE A 240 
 TYR   0.031   0.002   TYR A 428 
 ARG   0.007   0.000   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03942 (  156)
  hydrogen bonds       : angle       4.84856 (  438)
  SS BOND              : bond        0.00178 (    4)
  SS BOND              : angle       0.63280 (    8)
  covalent geometry    : bond        0.00365 ( 3560)
  covalent geometry    : angle       0.85904 ( 4822)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 LEU cc_start: 0.7472 (mt) cc_final: 0.7198 (mt)
REVERT: A  203 ARG cc_start: 0.6677 (OUTLIER) cc_final: 0.5249 (tpt-90)
REVERT: A  210 SER cc_start: 0.7835 (m) cc_final: 0.7539 (t)
REVERT: A  291 MET cc_start: 0.6038 (ptt) cc_final: 0.5248 (pmm)
REVERT: A  349 MET cc_start: 0.4723 (mmt) cc_final: 0.3441 (ptt)
REVERT: A  367 ASP cc_start: 0.7842 (t0) cc_final: 0.7588 (t0)
REVERT: A  433 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7822 (tm)
REVERT: A  482 MET cc_start: 0.7560 (ppp) cc_final: 0.7068 (mtt)
REVERT: A  501 LYS cc_start: 0.8573 (tppp) cc_final: 0.8340 (mmmt)
REVERT: B  109 TYR cc_start: 0.7779 (m-80) cc_final: 0.7460 (m-80)
  outliers start: 18
  outliers final: 11
  residues processed: 79
  average time/residue: 0.9448
  time to fit residues: 77.4933
Evaluate side-chains
  74 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  203 ARG
Chi-restraints excluded: chain A residue  279 GLN
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  108 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   chunk 42 optimal weight:    0.5980
   chunk 38 optimal weight:    0.2980
   chunk 35 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 39 optimal weight:    0.5980
   chunk 5 optimal weight:    0.2980
   chunk 11 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.184989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.170311 restraints weight = 7906.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.4367 rms_B_bonded: 3.54
r_work: 0.4273 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.4273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6578
moved from start:          0.4894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3564  Z= 0.169
  Angle     :  0.904  12.413   4830  Z= 0.437
  Chirality :  0.047   0.171    550
  Planarity :  0.005   0.061    587
  Dihedral  :  5.959  27.531    473
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.81 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 31.13 %
    Favored  : 64.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -2.06 (0.42), residues: 420
  helix: -0.01 (0.39), residues: 189
  sheet: -0.63 (0.84), residues: 35
  loop : -2.99 (0.43), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 449 
 HIS   0.001   0.000   HIS A 181 
 PHE   0.018   0.002   PHE A 224 
 TYR   0.032   0.002   TYR A 428 
 ARG   0.007   0.000   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03920 (  156)
  hydrogen bonds       : angle       4.95460 (  438)
  SS BOND              : bond        0.00238 (    4)
  SS BOND              : angle       0.67891 (    8)
  covalent geometry    : bond        0.00403 ( 3560)
  covalent geometry    : angle       0.90432 ( 4822)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 LEU cc_start: 0.7508 (mt) cc_final: 0.7237 (mt)
REVERT: A  203 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.5230 (tpt-90)
REVERT: A  210 SER cc_start: 0.7933 (m) cc_final: 0.7621 (t)
REVERT: A  349 MET cc_start: 0.4979 (mmt) cc_final: 0.3525 (ptt)
REVERT: A  367 ASP cc_start: 0.7824 (t0) cc_final: 0.7568 (t0)
REVERT: A  433 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7827 (tm)
REVERT: A  445 TYR cc_start: 0.6462 (t80) cc_final: 0.6211 (t80)
REVERT: A  482 MET cc_start: 0.7545 (ppp) cc_final: 0.7070 (mtt)
REVERT: A  501 LYS cc_start: 0.8607 (tppp) cc_final: 0.8370 (mmmt)
REVERT: B  109 TYR cc_start: 0.7767 (m-80) cc_final: 0.7483 (m-80)
  outliers start: 16
  outliers final: 10
  residues processed: 77
  average time/residue: 0.8746
  time to fit residues: 70.0832
Evaluate side-chains
  75 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  203 ARG
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  108 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 38 optimal weight:    0.0980
   chunk 36 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 40 optimal weight:    0.2980
   chunk 17 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 23 optimal weight:    0.1980
   overall best weight:    0.3580

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.184584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.169989 restraints weight = 8174.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.4358 rms_B_bonded: 3.56
r_work: 0.4262 rms_B_bonded: 4.50 restraints_weight: 0.5000
r_work (final): 0.4262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6577
moved from start:          0.5083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3564  Z= 0.159
  Angle     :  0.923  12.767   4830  Z= 0.442
  Chirality :  0.046   0.174    550
  Planarity :  0.005   0.061    587
  Dihedral  :  5.845  27.572    473
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 32.19 %
    Favored  : 63.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.93 (0.42), residues: 420
  helix:  0.12 (0.40), residues: 189
  sheet: -0.50 (0.86), residues: 35
  loop : -2.97 (0.44), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 449 
 HIS   0.001   0.000   HIS A 282 
 PHE   0.011   0.002   PHE A 224 
 TYR   0.029   0.002   TYR A 428 
 ARG   0.008   0.001   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03831 (  156)
  hydrogen bonds       : angle       4.93980 (  438)
  SS BOND              : bond        0.00201 (    4)
  SS BOND              : angle       0.73033 (    8)
  covalent geometry    : bond        0.00379 ( 3560)
  covalent geometry    : angle       0.92292 ( 4822)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 ARG cc_start: 0.6659 (OUTLIER) cc_final: 0.5193 (tpt-90)
REVERT: A  210 SER cc_start: 0.7865 (m) cc_final: 0.7551 (t)
REVERT: A  349 MET cc_start: 0.4748 (mmt) cc_final: 0.3466 (ptt)
REVERT: A  367 ASP cc_start: 0.7758 (t0) cc_final: 0.7539 (t0)
REVERT: A  433 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7879 (tm)
REVERT: A  445 TYR cc_start: 0.6462 (t80) cc_final: 0.6194 (t80)
REVERT: A  471 GLN cc_start: 0.7039 (pm20) cc_final: 0.6819 (pm20)
REVERT: A  482 MET cc_start: 0.7529 (ppp) cc_final: 0.7061 (mtt)
REVERT: A  501 LYS cc_start: 0.8635 (tppp) cc_final: 0.8403 (mmmt)
  outliers start: 15
  outliers final: 9
  residues processed: 78
  average time/residue: 0.8448
  time to fit residues: 68.6880
Evaluate side-chains
  74 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  203 ARG
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  102 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 6 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 33 optimal weight:    0.4980
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4491 r_free = 0.4491 target = 0.182381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.167221 restraints weight = 8172.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.4335 rms_B_bonded: 3.62
r_work: 0.4233 rms_B_bonded: 4.59 restraints_weight: 0.5000
r_work (final): 0.4233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6634
moved from start:          0.5220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   3564  Z= 0.183
  Angle     :  0.964  12.960   4830  Z= 0.460
  Chirality :  0.049   0.167    550
  Planarity :  0.005   0.060    587
  Dihedral  :  6.045  27.622    473
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 15.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.29 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 32.72 %
    Favored  : 63.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -2.04 (0.42), residues: 420
  helix: -0.04 (0.39), residues: 190
  sheet: -0.57 (0.87), residues: 35
  loop : -2.95 (0.44), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 453 
 HIS   0.001   0.001   HIS A 282 
 PHE   0.012   0.002   PHE A 296 
 TYR   0.030   0.002   TYR A 428 
 ARG   0.008   0.001   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03993 (  156)
  hydrogen bonds       : angle       4.99563 (  438)
  SS BOND              : bond        0.00276 (    4)
  SS BOND              : angle       0.78002 (    8)
  covalent geometry    : bond        0.00450 ( 3560)
  covalent geometry    : angle       0.96468 ( 4822)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3441.88 seconds
wall clock time: 59 minutes 54.30 seconds (3594.30 seconds total)