Starting phenix.real_space_refine
on Sat May 10 05:48:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cdp_16592/05_2025/8cdp_16592.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cdp_16592/05_2025/8cdp_16592.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cdp_16592/05_2025/8cdp_16592.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cdp_16592/05_2025/8cdp_16592.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cdp_16592/05_2025/8cdp_16592.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cdp_16592/05_2025/8cdp_16592.cif"
  }
  resolution = 3.4
  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=   0.000 sd=   0.001
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      30      5.16       5
     C    3290      2.51       5
     N     913      2.21       5
     O     967      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5200
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2472
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2472
          Classifications: {'peptide': 313}
          Link IDs: {'PTRANS': 17, 'TRANS': 295}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2728
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2728
          Classifications: {'peptide': 341}
          Link IDs: {'PTRANS': 16, 'TRANS': 324}
          Chain breaks: 1
  Residues with excluded nonbonded symmetry interactions: 6
    residue:
      pdb=" N   ASP A 366 " occ=0.00
      ... (6 atoms not shown)
      pdb=" OD2 ASP A 366 " occ=0.00
    residue:
      pdb=" N   ASP A 367 " occ=0.00
      ... (6 atoms not shown)
      pdb=" OD2 ASP A 367 " occ=0.00
    residue:
      pdb=" N   MET B 317 " occ=0.00
      ... (6 atoms not shown)
      pdb=" CE  MET B 317 " occ=0.00
    residue:
      pdb=" N   ALA B 318 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA B 318 " occ=0.00
    residue:
      pdb=" N   ARG B 382 " occ=0.00
      ... (9 atoms not shown)
      pdb=" NH2 ARG B 382 " occ=0.00
    residue:
      pdb=" N   ASP B 383 " occ=0.00
      ... (6 atoms not shown)
      pdb=" OD2 ASP B 383 " occ=0.00
  Time building chain proxies: 3.70, per 1000 atoms: 0.71
  Number of scatterers: 5200
  At special positions: 0
  Unit cell: (62.37, 64.8, 122.31, 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      30     16.00
     O     967      8.00
     N     913      7.00
     C    3290      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.16
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1246

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 5 sheets defined
      28.0% alpha, 17.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 196 through 217
      removed outlier: 3.795A  pdb=" N   ARG A 200 " --> pdb=" O   ASP A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 237
      removed outlier: 3.711A  pdb=" N   MET A 237 " --> pdb=" O   PRO A 234 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 234 through 237'
    Processing helix  chain 'A' and resid 246 through 257
      removed outlier: 3.648A  pdb=" N   VAL A 255 " --> pdb=" O   GLN A 251 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   ASN A 256 " --> pdb=" O   ARG A 252 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   HIS A 257 " --> pdb=" O   LEU A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 277
      removed outlier: 4.688A  pdb=" N   LYS A 272 " --> pdb=" O   SER A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 359
      removed outlier: 3.810A  pdb=" N   VAL A 353 " --> pdb=" O   ARG A 349 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   THR A 359 " --> pdb=" O   LEU A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 438
      removed outlier: 3.937A  pdb=" N   LYS A 437 " --> pdb=" O   ALA A 433 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   ALA A 438 " --> pdb=" O   ASN A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 468
      removed outlier: 3.639A  pdb=" N   VAL A 444 " --> pdb=" O   ASP A 440 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   GLU A 461 " --> pdb=" O   GLY A 457 " (cutoff:3.500A)
      removed outlier: 5.337A  pdb=" N   ASP A 462 " --> pdb=" O   LEU A 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 151
      removed outlier: 3.564A  pdb=" N   ARG B 150 " --> pdb=" O   GLY B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 235
    Processing helix  chain 'B' and resid 264 through 274
      removed outlier: 4.101A  pdb=" N   GLN B 274 " --> pdb=" O   HIS B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 285 through 298
      removed outlier: 3.790A  pdb=" N   ALA B 289 " --> pdb=" O   GLU B 285 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 375
      removed outlier: 3.523A  pdb=" N   ALA B 369 " --> pdb=" O   LYS B 365 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLU B 374 " --> pdb=" O   ASP B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 476
      removed outlier: 4.029A  pdb=" N   GLU B 476 " --> pdb=" O   ALA B 472 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 161
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 156 through 161
    current: chain 'A' and resid 259 through 263
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 259 through 263
    current: chain 'A' and resid 304 through 309
      removed outlier: 6.713A  pdb=" N   HIS A 306 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   VAL A 318 " --> pdb=" O   HIS A 306 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   ASP A 308 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 315 through 319
    current: chain 'A' and resid 337 through 344
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 337 through 344
    current: chain 'A' and resid 399 through 412
    Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 172
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 186 through 192
    current: chain 'B' and resid 174 through 179
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 174 through 179
    current: chain 'B' and resid 319 through 326
      removed outlier: 6.800A  pdb=" N   GLU B 324 " --> pdb=" O   THR B 332 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LYS B 330 " --> pdb=" O   ASN B 326 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 330 through 333
    current: chain 'B' and resid 353 through 360
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 353 through 360
    current: chain 'B' and resid 416 through 425
      removed outlier: 6.310A  pdb=" N   THR B 416 " --> pdb=" O   PRO B 446 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 245
    Processing sheet with id=AA4, first strand: chain 'A' and resid 362 through 365
    Processing sheet with id=AA5, first strand: chain 'B' and resid 378 through 380

    150 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: 1.27

  Time building geometry restraints manager: 1.38 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1240
        1.33 -     1.45: 1004
        1.45 -     1.57: 3012
        1.57 -     1.69: 0
        1.69 -     1.81: 49
  Bond restraints: 5305
  Sorted by residual:
  bond pdb=" N   ILE A 348 "
       pdb=" CA  ILE A 348 "
    ideal  model  delta    sigma   weight residual
    1.458  1.500 -0.043 1.27e-02 6.20e+03 1.14e+01
  bond pdb=" N   ARG A 350 "
       pdb=" CA  ARG A 350 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.21e-02 6.83e+03 6.06e+00
  bond pdb=" N   VAL B 312 "
       pdb=" CA  VAL B 312 "
    ideal  model  delta    sigma   weight residual
    1.457  1.484 -0.027 1.11e-02 8.12e+03 6.04e+00
  bond pdb=" C   GLN A 351 "
       pdb=" O   GLN A 351 "
    ideal  model  delta    sigma   weight residual
    1.237  1.209  0.028 1.17e-02 7.31e+03 5.55e+00
  bond pdb=" N   VAL B 397 "
       pdb=" CA  VAL B 397 "
    ideal  model  delta    sigma   weight residual
    1.455  1.480 -0.025 1.06e-02 8.90e+03 5.50e+00
  ... (remaining 5300 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.74: 7071
        2.74 -     5.49: 103
        5.49 -     8.23: 11
        8.23 -    10.97: 2
       10.97 -    13.72: 2
  Bond angle restraints: 7189
  Sorted by residual:
  angle pdb=" CB  GLU B 319 "
        pdb=" CG  GLU B 319 "
        pdb=" CD  GLU B 319 "
      ideal   model   delta    sigma   weight residual
     112.60  126.32  -13.72 1.70e+00 3.46e-01 6.51e+01
  angle pdb=" CB  GLU A 354 "
        pdb=" CG  GLU A 354 "
        pdb=" CD  GLU A 354 "
      ideal   model   delta    sigma   weight residual
     112.60  126.24  -13.64 1.70e+00 3.46e-01 6.44e+01
  angle pdb=" C   MET B 317 "
        pdb=" CA  MET B 317 "
        pdb=" CB  MET B 317 "
      ideal   model   delta    sigma   weight residual
     116.63  110.43    6.20 1.16e+00 7.43e-01 2.86e+01
  angle pdb=" N   GLN A 351 "
        pdb=" CA  GLN A 351 "
        pdb=" C   GLN A 351 "
      ideal   model   delta    sigma   weight residual
     111.28  105.71    5.57 1.09e+00 8.42e-01 2.61e+01
  angle pdb=" CA  ASP B 395 "
        pdb=" CB  ASP B 395 "
        pdb=" CG  ASP B 395 "
      ideal   model   delta    sigma   weight residual
     112.60  117.64   -5.04 1.00e+00 1.00e+00 2.54e+01
  ... (remaining 7184 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.95: 2942
       15.95 -    31.90: 236
       31.90 -    47.84: 44
       47.84 -    63.79: 19
       63.79 -    79.74: 6
  Dihedral angle restraints: 3247
    sinusoidal: 1330
      harmonic: 1917
  Sorted by residual:
  dihedral pdb=" CA  LYS B 365 "
           pdb=" C   LYS B 365 "
           pdb=" N   LYS B 366 "
           pdb=" CA  LYS B 366 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.95  -23.05     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  MET B 237 "
           pdb=" C   MET B 237 "
           pdb=" N   PRO B 238 "
           pdb=" CA  PRO B 238 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.97   20.03     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" C   ARG B 315 "
           pdb=" N   ARG B 315 "
           pdb=" CA  ARG B 315 "
           pdb=" CB  ARG B 315 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.69   -9.91     0      2.50e+00 1.60e-01 1.57e+01
  ... (remaining 3244 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 677
       0.059 -    0.119: 112
       0.119 -    0.178: 7
       0.178 -    0.238: 6
       0.238 -    0.297: 2
  Chirality restraints: 804
  Sorted by residual:
  chirality pdb=" CA  ARG B 315 "
            pdb=" N   ARG B 315 "
            pdb=" C   ARG B 315 "
            pdb=" CB  ARG B 315 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.21e+00
  chirality pdb=" CB  VAL B 312 "
            pdb=" CA  VAL B 312 "
            pdb=" CG1 VAL B 312 "
            pdb=" CG2 VAL B 312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.67e+00
  chirality pdb=" CA  VAL A 353 "
            pdb=" N   VAL A 353 "
            pdb=" C   VAL A 353 "
            pdb=" CB  VAL A 353 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.68   -0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 801 not shown)

  Planarity restraints: 928
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 315 "   -0.016 2.00e-02 2.50e+03   3.31e-02 1.09e+01
        pdb=" C   ARG B 315 "    0.057 2.00e-02 2.50e+03
        pdb=" O   ARG B 315 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ARG B 316 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 346 "   -0.014 2.00e-02 2.50e+03   2.65e-02 7.03e+00
        pdb=" C   PRO A 346 "    0.046 2.00e-02 2.50e+03
        pdb=" O   PRO A 346 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   PRO A 347 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 316 "    0.012 2.00e-02 2.50e+03   2.43e-02 5.91e+00
        pdb=" C   ARG B 316 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   ARG B 316 "    0.016 2.00e-02 2.50e+03
        pdb=" N   MET B 317 "    0.015 2.00e-02 2.50e+03
  ... (remaining 925 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 980
        2.78 -     3.31: 5055
        3.31 -     3.84: 8743
        3.84 -     4.37: 9875
        4.37 -     4.90: 16691
  Nonbonded interactions: 41344
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 309 "
            pdb=" OE2 GLU B 324 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   SER A 235 "
            pdb=" NH1 ARG A 238 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" OD1 ASP A 462 "
            pdb=" NH2 ARG A 465 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" NZ  LYS A 272 "
            pdb=" O   LEU A 458 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" OG1 THR A 185 "
            pdb=" O   ARG B 252 "
     model   vdw
     2.317 3.040
  ... (remaining 41339 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=0.00 max=1.00 mean=0.99
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:             1.120
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.760
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
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      :  0.003   0.043   5305  Z= 0.203
  Angle     :  0.783  13.716   7189  Z= 0.472
  Chirality :  0.048   0.297    804
  Planarity :  0.005   0.047    928
  Dihedral  : 12.956  79.740   2001
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  0.53 %
    Favored  : 99.11 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.12 (0.33), residues: 646
  helix:  2.13 (0.41), residues: 165
  sheet:  0.65 (0.38), residues: 175
  loop : -1.50 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 265 
 HIS   0.002   0.000   HIS A 332 
 PHE   0.011   0.001   PHE B 320 
 TYR   0.008   0.001   TYR B 251 
 ARG   0.020   0.001   ARG B 315 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11901 (  150)
  hydrogen bonds       : angle       6.04294 (  438)
  covalent geometry    : bond        0.00332 ( 5305)
  covalent geometry    : angle       0.78311 ( 7189)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 MET cc_start: 0.8835 (mtp) cc_final: 0.8616 (mtp)
REVERT: A  224 TYR cc_start: 0.8829 (t80) cc_final: 0.8579 (t80)
REVERT: B  223 MET cc_start: 0.8422 (mmp) cc_final: 0.8204 (mmp)
REVERT: B  235 MET cc_start: 0.9138 (mmt) cc_final: 0.8837 (mpp)
REVERT: B  237 MET cc_start: 0.8549 (mmm) cc_final: 0.8056 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 56
  average time/residue: 0.1847
  time to fit residues: 13.6392
Evaluate side-chains
  42 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 49 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 19 optimal weight:    0.1980
   chunk 30 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 328 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 = 0.3319 r_free = 0.3319 target = 0.056809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.043157 restraints weight = 20061.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 4.33
r_work: 0.2815 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.1060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   5305  Z= 0.196
  Angle     :  0.620   6.671   7189  Z= 0.317
  Chirality :  0.043   0.169    804
  Planarity :  0.004   0.033    928
  Dihedral  :  4.847  20.727    717
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  4.62 %
    Favored  : 94.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.04 (0.33), residues: 646
  helix:  2.38 (0.41), residues: 156
  sheet:  0.24 (0.36), residues: 195
  loop : -1.48 (0.34), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 209 
 HIS   0.015   0.001   HIS B 275 
 PHE   0.017   0.002   PHE B 321 
 TYR   0.010   0.001   TYR A 203 
 ARG   0.005   0.000   ARG B 361 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03730 (  150)
  hydrogen bonds       : angle       4.82065 (  438)
  covalent geometry    : bond        0.00428 ( 5305)
  covalent geometry    : angle       0.61972 ( 7189)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 45
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
REVERT: A  224 TYR cc_start: 0.8974 (t80) cc_final: 0.8767 (t80)
REVERT: B  219 MET cc_start: 0.8722 (tmm) cc_final: 0.8511 (tmm)
REVERT: B  235 MET cc_start: 0.9377 (mmt) cc_final: 0.9043 (mpp)
REVERT: B  237 MET cc_start: 0.8812 (mmm) cc_final: 0.8524 (mmm)
REVERT: B  367 ARG cc_start: 0.9405 (ptp90) cc_final: 0.9052 (mtm110)
  outliers start: 3
  outliers final: 3
  residues processed: 46
  average time/residue: 0.2126
  time to fit residues: 12.7363
Evaluate side-chains
  40 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 CYS
Chi-restraints excluded: chain B residue  362 HIS
Chi-restraints excluded: chain B residue  389 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 60 optimal weight:    8.9990
   chunk 54 optimal weight:    8.9990
   chunk 48 optimal weight:    6.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
B 258 ASN
** B 328 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 = 0.3184 r_free = 0.3184 target = 0.053350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.039387 restraints weight = 20695.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.2773 rms_B_bonded: 4.50
r_work: 0.2634 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.2634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043   5305  Z= 0.313
  Angle     :  0.716   9.600   7189  Z= 0.362
  Chirality :  0.045   0.166    804
  Planarity :  0.004   0.035    928
  Dihedral  :  5.323  27.912    717
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  7.82 %
    Favored  : 90.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.54 (0.32), residues: 646
  helix:  1.64 (0.40), residues: 157
  sheet: -0.26 (0.39), residues: 177
  loop : -1.50 (0.33), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 407 
 HIS   0.011   0.002   HIS B 275 
 PHE   0.024   0.002   PHE B 225 
 TYR   0.016   0.002   TYR B 250 
 ARG   0.005   0.001   ARG B 367 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04060 (  150)
  hydrogen bonds       : angle       4.96754 (  438)
  covalent geometry    : bond        0.00677 ( 5305)
  covalent geometry    : angle       0.71559 ( 7189)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.974 
Fit side-chains
REVERT: A  152 MET cc_start: 0.7916 (ptt) cc_final: 0.6443 (pmm)
REVERT: A  216 ASN cc_start: 0.9325 (m110) cc_final: 0.9064 (p0)
REVERT: A  224 TYR cc_start: 0.8965 (t80) cc_final: 0.8755 (t80)
REVERT: B  219 MET cc_start: 0.8672 (tmm) cc_final: 0.8409 (tmm)
REVERT: B  237 MET cc_start: 0.8855 (mmm) cc_final: 0.8575 (mmm)
REVERT: B  315 ARG cc_start: 0.9361 (ttt90) cc_final: 0.8944 (ttm110)
  outliers start: 7
  outliers final: 5
  residues processed: 43
  average time/residue: 0.1946
  time to fit residues: 11.1956
Evaluate side-chains
  43 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 CYS
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain B residue  362 HIS
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  393 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 56 optimal weight:    8.9990
   chunk 0 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** B 328 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 = 0.3231 r_free = 0.3231 target = 0.055895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.041139 restraints weight = 20139.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.2805 rms_B_bonded: 4.77
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5305  Z= 0.142
  Angle     :  0.584   8.906   7189  Z= 0.294
  Chirality :  0.042   0.174    804
  Planarity :  0.003   0.032    928
  Dihedral  :  4.937  27.011    717
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  9.06 %
    Favored  : 89.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.24 (0.33), residues: 646
  helix:  2.14 (0.41), residues: 156
  sheet: -0.03 (0.37), residues: 195
  loop : -1.56 (0.34), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 443 
 HIS   0.010   0.001   HIS B 275 
 PHE   0.010   0.001   PHE A 283 
 TYR   0.009   0.001   TYR B 251 
 ARG   0.003   0.000   ARG B 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03263 (  150)
  hydrogen bonds       : angle       4.52157 (  438)
  covalent geometry    : bond        0.00316 ( 5305)
  covalent geometry    : angle       0.58390 ( 7189)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7749 (ptt) cc_final: 0.6311 (pmm)
REVERT: A  216 ASN cc_start: 0.9228 (m110) cc_final: 0.8963 (p0)
REVERT: A  224 TYR cc_start: 0.8803 (t80) cc_final: 0.8474 (t80)
REVERT: B  219 MET cc_start: 0.8461 (tmm) cc_final: 0.8066 (tmm)
REVERT: B  237 MET cc_start: 0.8356 (mmm) cc_final: 0.8024 (mmm)
REVERT: B  300 MET cc_start: 0.6273 (mmm) cc_final: 0.5974 (tpp)
REVERT: B  315 ARG cc_start: 0.9317 (ttt90) cc_final: 0.8879 (ttm110)
  outliers start: 7
  outliers final: 3
  residues processed: 47
  average time/residue: 0.1818
  time to fit residues: 11.5057
Evaluate side-chains
  43 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  269 CYS
Chi-restraints excluded: chain B residue  362 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0170
   chunk 0 optimal weight:    4.9990
   chunk 47 optimal weight:    9.9990
   chunk 58 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.7018

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.056367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.041766 restraints weight = 19549.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.2830 rms_B_bonded: 4.74
r_work: 0.2686 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5305  Z= 0.112
  Angle     :  0.560   9.097   7189  Z= 0.281
  Chirality :  0.042   0.171    804
  Planarity :  0.003   0.030    928
  Dihedral  :  4.703  24.154    717
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 10.83 %
    Favored  : 88.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.15 (0.33), residues: 646
  helix:  2.40 (0.41), residues: 156
  sheet: -0.07 (0.37), residues: 198
  loop : -1.56 (0.34), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 209 
 HIS   0.009   0.001   HIS B 275 
 PHE   0.007   0.001   PHE B 225 
 TYR   0.013   0.001   TYR B 372 
 ARG   0.005   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03015 (  150)
  hydrogen bonds       : angle       4.30952 (  438)
  covalent geometry    : bond        0.00252 ( 5305)
  covalent geometry    : angle       0.55961 ( 7189)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7783 (ptt) cc_final: 0.6339 (pmm)
REVERT: A  216 ASN cc_start: 0.9290 (m110) cc_final: 0.9021 (p0)
REVERT: A  224 TYR cc_start: 0.8856 (t80) cc_final: 0.8570 (t80)
REVERT: B  219 MET cc_start: 0.8637 (tmm) cc_final: 0.8202 (tmm)
REVERT: B  237 MET cc_start: 0.8755 (mmm) cc_final: 0.8427 (mmm)
  outliers start: 5
  outliers final: 5
  residues processed: 44
  average time/residue: 0.1871
  time to fit residues: 11.0837
Evaluate side-chains
  43 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  269 CYS
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain B residue  362 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 10 optimal weight:    0.4980
   chunk 26 optimal weight:    0.8980
   chunk 17 optimal weight:    5.9990
   chunk 44 optimal weight:    7.9990
   chunk 47 optimal weight:    0.2980
   chunk 54 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
B 268 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.056353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.041744 restraints weight = 19843.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 4.79
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5305  Z= 0.110
  Angle     :  0.560   8.666   7189  Z= 0.276
  Chirality :  0.041   0.167    804
  Planarity :  0.003   0.041    928
  Dihedral  :  4.599  21.836    717
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 11.90 %
    Favored  : 87.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.10 (0.33), residues: 646
  helix:  2.48 (0.40), residues: 156
  sheet: -0.04 (0.37), residues: 198
  loop : -1.56 (0.34), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 407 
 HIS   0.007   0.001   HIS B 275 
 PHE   0.006   0.001   PHE A 283 
 TYR   0.007   0.001   TYR A 247 
 ARG   0.008   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02896 (  150)
  hydrogen bonds       : angle       4.23303 (  438)
  covalent geometry    : bond        0.00247 ( 5305)
  covalent geometry    : angle       0.55968 ( 7189)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.622 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7739 (ptt) cc_final: 0.6328 (pmm)
REVERT: A  216 ASN cc_start: 0.9196 (m110) cc_final: 0.8947 (p0)
REVERT: A  224 TYR cc_start: 0.8763 (t80) cc_final: 0.8340 (t80)
REVERT: B  219 MET cc_start: 0.8479 (tmm) cc_final: 0.8037 (tmm)
REVERT: B  237 MET cc_start: 0.8392 (mmm) cc_final: 0.8013 (mmm)
REVERT: B  315 ARG cc_start: 0.9274 (ttt90) cc_final: 0.8815 (ttm110)
  outliers start: 5
  outliers final: 4
  residues processed: 44
  average time/residue: 0.1929
  time to fit residues: 11.3525
Evaluate side-chains
  42 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 CYS
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain B residue  362 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 3 optimal weight:    7.9990
   chunk 48 optimal weight:    0.0980
   chunk 2 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0970
   chunk 60 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.056272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.041816 restraints weight = 19596.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.2837 rms_B_bonded: 4.75
r_work: 0.2693 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5305  Z= 0.112
  Angle     :  0.556   8.819   7189  Z= 0.272
  Chirality :  0.043   0.281    804
  Planarity :  0.003   0.031    928
  Dihedral  :  4.536  19.637    717
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 11.72 %
    Favored  : 86.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.33), residues: 646
  helix:  2.54 (0.40), residues: 156
  sheet: -0.02 (0.37), residues: 198
  loop : -1.53 (0.34), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 407 
 HIS   0.007   0.001   HIS B 275 
 PHE   0.010   0.001   PHE B 321 
 TYR   0.008   0.001   TYR B 372 
 ARG   0.006   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02837 (  150)
  hydrogen bonds       : angle       4.25407 (  438)
  covalent geometry    : bond        0.00251 ( 5305)
  covalent geometry    : angle       0.55597 ( 7189)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7779 (ptt) cc_final: 0.6370 (pmm)
REVERT: A  216 ASN cc_start: 0.9284 (m110) cc_final: 0.9018 (p0)
REVERT: A  224 TYR cc_start: 0.8825 (t80) cc_final: 0.8530 (t80)
REVERT: B  219 MET cc_start: 0.8627 (tmm) cc_final: 0.8182 (tmm)
REVERT: B  237 MET cc_start: 0.8768 (mmm) cc_final: 0.8431 (mmm)
REVERT: B  315 ARG cc_start: 0.9294 (ttt90) cc_final: 0.8853 (ttm110)
  outliers start: 10
  outliers final: 8
  residues processed: 47
  average time/residue: 0.1840
  time to fit residues: 11.6242
Evaluate side-chains
  46 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  269 CYS
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  223 MET
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain B residue  362 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   chunk 57 optimal weight:    8.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.055835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.041405 restraints weight = 19850.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.2822 rms_B_bonded: 4.75
r_work: 0.2677 rms_B_bonded: 4.98 restraints_weight: 0.5000
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5305  Z= 0.148
  Angle     :  0.581  13.636   7189  Z= 0.281
  Chirality :  0.043   0.375    804
  Planarity :  0.003   0.031    928
  Dihedral  :  4.553  19.759    717
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 12.08 %
    Favored  : 85.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.08 (0.33), residues: 646
  helix:  2.53 (0.41), residues: 156
  sheet: -0.09 (0.37), residues: 198
  loop : -1.52 (0.34), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 407 
 HIS   0.006   0.001   HIS B 275 
 PHE   0.009   0.001   PHE B 225 
 TYR   0.007   0.001   TYR B 251 
 ARG   0.005   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02967 (  150)
  hydrogen bonds       : angle       4.26130 (  438)
  covalent geometry    : bond        0.00326 ( 5305)
  covalent geometry    : angle       0.58053 ( 7189)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7771 (ptt) cc_final: 0.6363 (pmm)
REVERT: A  216 ASN cc_start: 0.9292 (m110) cc_final: 0.9033 (p0)
REVERT: A  224 TYR cc_start: 0.8857 (t80) cc_final: 0.8503 (t80)
REVERT: B  219 MET cc_start: 0.8677 (tmm) cc_final: 0.8209 (tmm)
REVERT: B  237 MET cc_start: 0.8793 (mmm) cc_final: 0.8470 (mmm)
REVERT: B  315 ARG cc_start: 0.9329 (ttt90) cc_final: 0.8876 (ttm110)
REVERT: B  320 PHE cc_start: 0.8496 (m-10) cc_final: 0.8294 (m-10)
  outliers start: 11
  outliers final: 10
  residues processed: 46
  average time/residue: 0.1883
  time to fit residues: 11.6203
Evaluate side-chains
  49 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  269 CYS
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  223 MET
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  362 HIS
Chi-restraints excluded: chain B residue  389 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 55 optimal weight:    0.4980
   chunk 7 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 13 optimal weight:    9.9990
   chunk 27 optimal weight:    0.0010
   chunk 15 optimal weight:    0.0970
   chunk 59 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN
B 176 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.056553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.042137 restraints weight = 19732.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.2847 rms_B_bonded: 4.76
r_work: 0.2704 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5305  Z= 0.099
  Angle     :  0.579  14.623   7189  Z= 0.277
  Chirality :  0.043   0.367    804
  Planarity :  0.003   0.051    928
  Dihedral  :  4.431  19.297    717
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.79 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.33), residues: 646
  helix:  2.62 (0.41), residues: 156
  sheet: -0.04 (0.37), residues: 198
  loop : -1.46 (0.34), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 443 
 HIS   0.006   0.001   HIS B 275 
 PHE   0.010   0.001   PHE B 321 
 TYR   0.007   0.001   TYR A 247 
 ARG   0.011   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02817 (  150)
  hydrogen bonds       : angle       4.22675 (  438)
  covalent geometry    : bond        0.00223 ( 5305)
  covalent geometry    : angle       0.57866 ( 7189)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7763 (ptt) cc_final: 0.6389 (pmm)
REVERT: A  216 ASN cc_start: 0.9283 (m110) cc_final: 0.9000 (p0)
REVERT: A  224 TYR cc_start: 0.8824 (t80) cc_final: 0.8479 (t80)
REVERT: B  219 MET cc_start: 0.8663 (tmm) cc_final: 0.8171 (tmm)
REVERT: B  237 MET cc_start: 0.8753 (mmm) cc_final: 0.8398 (mmm)
REVERT: B  315 ARG cc_start: 0.9307 (ttt90) cc_final: 0.8858 (ttm110)
REVERT: B  320 PHE cc_start: 0.8548 (m-10) cc_final: 0.8342 (m-10)
REVERT: B  478 MET cc_start: 0.7200 (tpt) cc_final: 0.6869 (tpt)
  outliers start: 9
  outliers final: 8
  residues processed: 49
  average time/residue: 0.1949
  time to fit residues: 12.9239
Evaluate side-chains
  48 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  269 CYS
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  362 HIS
Chi-restraints excluded: chain B residue  389 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 28 optimal weight:    0.6980
   chunk 1 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 25 optimal weight:    0.4980
   chunk 34 optimal weight:    5.9990
   overall best weight:    0.8386

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.056480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.041996 restraints weight = 19693.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 4.78
r_work: 0.2698 rms_B_bonded: 5.00 restraints_weight: 0.5000
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5305  Z= 0.122
  Angle     :  0.628  14.710   7189  Z= 0.303
  Chirality :  0.044   0.344    804
  Planarity :  0.003   0.040    928
  Dihedral  :  4.443  19.202    717
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 13.32 %
    Favored  : 84.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.00 (0.33), residues: 646
  helix:  2.62 (0.41), residues: 155
  sheet: -0.11 (0.36), residues: 205
  loop : -1.43 (0.34), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 407 
 HIS   0.006   0.001   HIS B 275 
 PHE   0.006   0.001   PHE B 225 
 TYR   0.015   0.001   TYR A 203 
 ARG   0.009   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03064 (  150)
  hydrogen bonds       : angle       4.42217 (  438)
  covalent geometry    : bond        0.00275 ( 5305)
  covalent geometry    : angle       0.62838 ( 7189)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.593 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7764 (ptt) cc_final: 0.6392 (pmm)
REVERT: A  216 ASN cc_start: 0.9286 (m110) cc_final: 0.9000 (p0)
REVERT: A  224 TYR cc_start: 0.8841 (t80) cc_final: 0.8502 (t80)
REVERT: B  219 MET cc_start: 0.8656 (tmm) cc_final: 0.8180 (tmm)
REVERT: B  237 MET cc_start: 0.8732 (mmm) cc_final: 0.8384 (mmm)
REVERT: B  315 ARG cc_start: 0.9317 (ttt90) cc_final: 0.8866 (ttm110)
REVERT: B  478 MET cc_start: 0.7321 (tpt) cc_final: 0.6954 (tpt)
  outliers start: 10
  outliers final: 9
  residues processed: 48
  average time/residue: 0.1804
  time to fit residues: 11.5379
Evaluate side-chains
  49 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  269 CYS
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  223 MET
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  362 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 42 optimal weight:    7.9990
   chunk 26 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.054623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.040359 restraints weight = 20313.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.2800 rms_B_bonded: 4.72
r_work: 0.2654 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5305  Z= 0.220
  Angle     :  0.685  14.091   7189  Z= 0.332
  Chirality :  0.045   0.322    804
  Planarity :  0.004   0.049    928
  Dihedral  :  4.647  19.930    717
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 13.68 %
    Favored  : 84.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.18 (0.33), residues: 646
  helix:  2.42 (0.41), residues: 155
  sheet: -0.23 (0.36), residues: 203
  loop : -1.50 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 209 
 HIS   0.005   0.001   HIS B 275 
 PHE   0.012   0.001   PHE B 225 
 TYR   0.014   0.002   TYR A 203 
 ARG   0.010   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03398 (  150)
  hydrogen bonds       : angle       4.54253 (  438)
  covalent geometry    : bond        0.00482 ( 5305)
  covalent geometry    : angle       0.68497 ( 7189)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2749.90 seconds
wall clock time: 48 minutes 27.87 seconds (2907.87 seconds total)