Starting phenix.real_space_refine
on Fri Aug 22 15:46:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cdp_16592/08_2025/8cdp_16592.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cdp_16592/08_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_16592/08_2025/8cdp_16592.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cdp_16592/08_2025/8cdp_16592.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cdp_16592/08_2025/8cdp_16592.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cdp_16592/08_2025/8cdp_16592.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.12, per 1000 atoms: 0.22
  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: 0.28
  Conformation dependent library (CDL) restraints added in 130.0 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  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: 0.11
  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: 0.62

  Time building geometry restraints manager: 0.39 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:             1.620
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     5.070
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.940
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.020   0.001   ARG B 315 
 TYR   0.008   0.001   TYR B 251 
 PHE   0.011   0.001   PHE B 320 
 TRP   0.015   0.002   TRP B 265 
 HIS   0.002   0.000   HIS A 332 

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

*********************** 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  : 0.165 
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: 0.0624
  time to fit residues: 4.6886
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  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    0.0870
   chunk 64 optimal weight:    6.9990
   overall best weight:    1.3562

-------------------------------------------------------------------------------
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 = 0.3284 r_free = 0.3284 target = 0.056406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.042355 restraints weight = 20039.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.2894 rms_B_bonded: 4.49
r_work: 0.2754 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.1040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5305  Z= 0.158
  Angle     :  0.592   6.630   7189  Z= 0.303
  Chirality :  0.042   0.164    804
  Planarity :  0.004   0.032    928
  Dihedral  :  4.764  20.750    717
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  4.26 %
    Favored  : 95.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.33), residues: 646
  helix:  2.45 (0.41), residues: 156
  sheet:  0.26 (0.36), residues: 195
  loop : -1.46 (0.34), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 361 
 TYR   0.011   0.001   TYR A 203 
 PHE   0.018   0.002   PHE B 321 
 TRP   0.012   0.002   TRP A 209 
 HIS   0.015   0.001   HIS B 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 5305)
  covalent geometry    : angle       0.59206 ( 7189)
  hydrogen bonds       : bond        0.03547 (  150)
  hydrogen bonds       : angle       4.76601 (  438)

*********************** 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
  49 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
REVERT: A  224 TYR cc_start: 0.8926 (t80) cc_final: 0.8695 (t80)
REVERT: B  219 MET cc_start: 0.8666 (tmm) cc_final: 0.8357 (tmm)
REVERT: B  235 MET cc_start: 0.9366 (mmt) cc_final: 0.9023 (mpp)
REVERT: B  237 MET cc_start: 0.8837 (mmm) cc_final: 0.8573 (mmm)
REVERT: B  367 ARG cc_start: 0.9419 (ptp90) cc_final: 0.9066 (mtm110)
  outliers start: 3
  outliers final: 3
  residues processed: 47
  average time/residue: 0.0861
  time to fit residues: 5.1635
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  : 0.122 
-------------------------------------------------------------------------------
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 4 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 53 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9980
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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 = 0.3211 r_free = 0.3211 target = 0.054704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.040328 restraints weight = 20121.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.2796 rms_B_bonded: 4.67
r_work: 0.2652 rms_B_bonded: 4.86 restraints_weight: 0.5000
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   5305  Z= 0.245
  Angle     :  0.657   9.287   7189  Z= 0.331
  Chirality :  0.043   0.171    804
  Planarity :  0.004   0.032    928
  Dihedral  :  5.105  30.813    717
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  7.46 %
    Favored  : 91.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.28 (0.33), residues: 646
  helix:  1.95 (0.40), residues: 158
  sheet: -0.29 (0.36), residues: 202
  loop : -1.33 (0.35), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 361 
 TYR   0.014   0.002   TYR B 250 
 PHE   0.020   0.002   PHE B 225 
 TRP   0.016   0.002   TRP B 407 
 HIS   0.011   0.001   HIS B 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 ( 5305)
  covalent geometry    : angle       0.65739 ( 7189)
  hydrogen bonds       : bond        0.03759 (  150)
  hydrogen bonds       : angle       4.77977 (  438)

*********************** 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
  48 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: A  216 ASN cc_start: 0.9303 (m110) cc_final: 0.9030 (p0)
REVERT: A  224 TYR cc_start: 0.8980 (t80) cc_final: 0.8710 (t80)
REVERT: B  219 MET cc_start: 0.8628 (tmm) cc_final: 0.8380 (tmm)
REVERT: B  237 MET cc_start: 0.8863 (mmm) cc_final: 0.8574 (mmm)
  outliers start: 6
  outliers final: 3
  residues processed: 44
  average time/residue: 0.0737
  time to fit residues: 4.3143
Evaluate side-chains
  41 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 1 optimal weight:    5.9990
   chunk 28 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    1.7184

-------------------------------------------------------------------------------
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 = 0.3220 r_free = 0.3220 target = 0.055371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.040843 restraints weight = 20005.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.2797 rms_B_bonded: 4.70
r_work: 0.2653 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.1668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5305  Z= 0.180
  Angle     :  0.602   9.390   7189  Z= 0.302
  Chirality :  0.042   0.171    804
  Planarity :  0.003   0.030    928
  Dihedral  :  4.964  27.690    717
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  8.53 %
    Favored  : 90.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.33), residues: 646
  helix:  2.23 (0.41), residues: 156
  sheet: -0.02 (0.37), residues: 195
  loop : -1.51 (0.34), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 315 
 TYR   0.010   0.001   TYR B 372 
 PHE   0.013   0.001   PHE B 225 
 TRP   0.012   0.002   TRP B 443 
 HIS   0.010   0.001   HIS B 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 5305)
  covalent geometry    : angle       0.60192 ( 7189)
  hydrogen bonds       : bond        0.03356 (  150)
  hydrogen bonds       : angle       4.50842 (  438)

*********************** 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
  46 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7825 (ptt) cc_final: 0.6352 (pmm)
REVERT: A  216 ASN cc_start: 0.9317 (m110) cc_final: 0.9037 (p0)
REVERT: A  224 TYR cc_start: 0.8906 (t80) cc_final: 0.8643 (t80)
REVERT: B  219 MET cc_start: 0.8602 (tmm) cc_final: 0.8214 (tmm)
REVERT: B  237 MET cc_start: 0.8799 (mmm) cc_final: 0.8486 (mmm)
REVERT: B  315 ARG cc_start: 0.9377 (ttt90) cc_final: 0.8953 (ttm110)
  outliers start: 6
  outliers final: 3
  residues processed: 43
  average time/residue: 0.0844
  time to fit residues: 4.8124
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  : 0.196 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 58 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 26 optimal weight:    7.9990
   chunk 0 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
** 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 = 0.3242 r_free = 0.3242 target = 0.056033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.041477 restraints weight = 19872.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.2823 rms_B_bonded: 4.77
r_work: 0.2676 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5305  Z= 0.121
  Angle     :  0.555   8.603   7189  Z= 0.277
  Chirality :  0.042   0.170    804
  Planarity :  0.003   0.028    928
  Dihedral  :  4.735  25.368    717
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  :  9.77 %
    Favored  : 88.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.33), residues: 646
  helix:  2.45 (0.41), residues: 156
  sheet: -0.01 (0.37), residues: 195
  loop : -1.49 (0.34), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 220 
 TYR   0.013   0.001   TYR B 372 
 PHE   0.009   0.001   PHE B 225 
 TRP   0.011   0.001   TRP B 443 
 HIS   0.008   0.001   HIS B 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 5305)
  covalent geometry    : angle       0.55512 ( 7189)
  hydrogen bonds       : bond        0.03003 (  150)
  hydrogen bonds       : angle       4.32821 (  438)

*********************** 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
  49 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7817 (ptt) cc_final: 0.6366 (pmm)
REVERT: A  216 ASN cc_start: 0.9294 (m110) cc_final: 0.9022 (p0)
REVERT: A  224 TYR cc_start: 0.8885 (t80) cc_final: 0.8553 (t80)
REVERT: B  219 MET cc_start: 0.8622 (tmm) cc_final: 0.8211 (tmm)
REVERT: B  237 MET cc_start: 0.8762 (mmm) cc_final: 0.8438 (mmm)
REVERT: B  315 ARG cc_start: 0.9335 (ttt90) cc_final: 0.8891 (ttm110)
  outliers start: 9
  outliers final: 7
  residues processed: 45
  average time/residue: 0.0831
  time to fit residues: 4.9760
Evaluate side-chains
  48 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  269 CYS
Chi-restraints excluded: chain A residue  455 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 0 optimal weight:    4.9990
   chunk 56 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 17 optimal weight:    0.3980
   chunk 45 optimal weight:    7.9990
   chunk 13 optimal weight:   10.0000
   chunk 50 optimal weight:    4.9990
   overall best weight:    2.4788

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3201 r_free = 0.3201 target = 0.054545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.040098 restraints weight = 20410.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.2775 rms_B_bonded: 4.73
r_work: 0.2631 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.2631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.1971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   5305  Z= 0.242
  Angle     :  0.637   8.940   7189  Z= 0.315
  Chirality :  0.044   0.289    804
  Planarity :  0.003   0.036    928
  Dihedral  :  4.920  22.046    717
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 10.30 %
    Favored  : 87.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.33), residues: 646
  helix:  2.27 (0.41), residues: 155
  sheet: -0.19 (0.37), residues: 198
  loop : -1.54 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 349 
 TYR   0.012   0.001   TYR B 250 
 PHE   0.016   0.002   PHE B 225 
 TRP   0.013   0.002   TRP A 209 
 HIS   0.007   0.001   HIS B 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00528 ( 5305)
  covalent geometry    : angle       0.63676 ( 7189)
  hydrogen bonds       : bond        0.03394 (  150)
  hydrogen bonds       : angle       4.47806 (  438)

*********************** 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
  52 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7881 (ptt) cc_final: 0.6442 (pmm)
REVERT: A  224 TYR cc_start: 0.8917 (t80) cc_final: 0.8579 (t80)
REVERT: B  219 MET cc_start: 0.8681 (tmm) cc_final: 0.8225 (tmm)
REVERT: B  237 MET cc_start: 0.8794 (mmm) cc_final: 0.8471 (mmm)
REVERT: B  315 ARG cc_start: 0.9373 (ttt90) cc_final: 0.8929 (ttm110)
REVERT: B  320 PHE cc_start: 0.8491 (m-10) cc_final: 0.8270 (m-10)
  outliers start: 11
  outliers final: 9
  residues processed: 48
  average time/residue: 0.0643
  time to fit residues: 4.1382
Evaluate side-chains
  48 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain B residue  389 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 60 optimal weight:    4.9990
   chunk 28 optimal weight:    0.4980
   chunk 31 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 42 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    2.0586

-------------------------------------------------------------------------------
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 = 0.3204 r_free = 0.3204 target = 0.054673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.040228 restraints weight = 20239.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.2781 rms_B_bonded: 4.72
r_work: 0.2633 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.2633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   5305  Z= 0.209
  Angle     :  0.633  12.354   7189  Z= 0.309
  Chirality :  0.043   0.252    804
  Planarity :  0.004   0.053    928
  Dihedral  :  4.905  21.513    717
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 11.72 %
    Favored  : 86.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.34 (0.33), residues: 646
  helix:  2.17 (0.41), residues: 155
  sheet: -0.22 (0.37), residues: 198
  loop : -1.57 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 349 
 TYR   0.010   0.001   TYR B 250 
 PHE   0.013   0.001   PHE B 225 
 TRP   0.013   0.002   TRP B 443 
 HIS   0.007   0.001   HIS B 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 5305)
  covalent geometry    : angle       0.63276 ( 7189)
  hydrogen bonds       : bond        0.03358 (  150)
  hydrogen bonds       : angle       4.49610 (  438)

*********************** 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: 11
    poor density    : 39
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7870 (ptt) cc_final: 0.6460 (pmm)
REVERT: A  216 ASN cc_start: 0.9325 (m110) cc_final: 0.9105 (p0)
REVERT: A  224 TYR cc_start: 0.8886 (t80) cc_final: 0.8609 (t80)
REVERT: B  219 MET cc_start: 0.8683 (tmm) cc_final: 0.8213 (tmm)
REVERT: B  237 MET cc_start: 0.8786 (mmm) cc_final: 0.8481 (mmm)
REVERT: B  315 ARG cc_start: 0.9373 (ttt90) cc_final: 0.8920 (ttm110)
REVERT: B  320 PHE cc_start: 0.8478 (m-10) cc_final: 0.8274 (m-10)
  outliers start: 11
  outliers final: 9
  residues processed: 47
  average time/residue: 0.0792
  time to fit residues: 5.0044
Evaluate side-chains
  48 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
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  294 LEU
Chi-restraints excluded: chain B residue  362 HIS
Chi-restraints excluded: chain B residue  389 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 7 optimal weight:    0.2980
   chunk 3 optimal weight:    5.9990
   chunk 12 optimal weight:    0.6980
   chunk 21 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3236 r_free = 0.3236 target = 0.055876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.041386 restraints weight = 19675.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.2820 rms_B_bonded: 4.72
r_work: 0.2673 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.2038

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= 0.114
  Angle     :  0.606  11.588   7189  Z= 0.290
  Chirality :  0.043   0.218    804
  Planarity :  0.003   0.051    928
  Dihedral  :  4.651  20.863    717
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 12.08 %
    Favored  : 86.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.33), residues: 646
  helix:  2.42 (0.41), residues: 155
  sheet: -0.14 (0.37), residues: 198
  loop : -1.51 (0.34), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 349 
 TYR   0.007   0.001   TYR B 251 
 PHE   0.007   0.001   PHE A 283 
 TRP   0.012   0.001   TRP B 443 
 HIS   0.007   0.001   HIS B 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 5305)
  covalent geometry    : angle       0.60608 ( 7189)
  hydrogen bonds       : bond        0.03077 (  150)
  hydrogen bonds       : angle       4.37273 (  438)

*********************** 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
  52 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7760 (ptt) cc_final: 0.6378 (pmm)
REVERT: A  216 ASN cc_start: 0.9302 (m110) cc_final: 0.9075 (p0)
REVERT: A  224 TYR cc_start: 0.8847 (t80) cc_final: 0.8577 (t80)
REVERT: B  219 MET cc_start: 0.8651 (tmm) cc_final: 0.8172 (tmm)
REVERT: B  237 MET cc_start: 0.8773 (mmm) cc_final: 0.8455 (mmm)
REVERT: B  315 ARG cc_start: 0.9353 (ttt90) cc_final: 0.8899 (ttm110)
  outliers start: 10
  outliers final: 7
  residues processed: 48
  average time/residue: 0.0726
  time to fit residues: 4.6242
Evaluate side-chains
  45 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
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  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:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   chunk 63 optimal weight:    0.5980
   chunk 60 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0970
   chunk 18 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.3252 r_free = 0.3252 target = 0.056348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.041724 restraints weight = 19750.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 4.77
r_work: 0.2688 rms_B_bonded: 5.00 restraints_weight: 0.5000
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5305  Z= 0.114
  Angle     :  0.599  11.417   7189  Z= 0.292
  Chirality :  0.043   0.194    804
  Planarity :  0.003   0.030    928
  Dihedral  :  4.504  20.185    717
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.97 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.33), residues: 646
  helix:  2.42 (0.41), residues: 156
  sheet: -0.07 (0.37), residues: 203
  loop : -1.47 (0.34), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 349 
 TYR   0.014   0.001   TYR A 203 
 PHE   0.013   0.001   PHE B 321 
 TRP   0.011   0.001   TRP B 443 
 HIS   0.006   0.001   HIS B 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 5305)
  covalent geometry    : angle       0.59923 ( 7189)
  hydrogen bonds       : bond        0.03247 (  150)
  hydrogen bonds       : angle       4.47385 (  438)

*********************** 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
  48 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7762 (ptt) cc_final: 0.6408 (pmm)
REVERT: A  216 ASN cc_start: 0.9284 (m110) cc_final: 0.9071 (p0)
REVERT: A  224 TYR cc_start: 0.8854 (t80) cc_final: 0.8541 (t80)
REVERT: B  219 MET cc_start: 0.8640 (tmm) cc_final: 0.8159 (tmm)
REVERT: B  237 MET cc_start: 0.8808 (mmm) cc_final: 0.8472 (mmm)
REVERT: B  315 ARG cc_start: 0.9339 (ttt90) cc_final: 0.8891 (ttm110)
REVERT: B  320 PHE cc_start: 0.8493 (m-10) cc_final: 0.8277 (m-10)
  outliers start: 9
  outliers final: 7
  residues processed: 45
  average time/residue: 0.0822
  time to fit residues: 4.9120
Evaluate side-chains
  45 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 59 optimal weight:    8.9990
   chunk 13 optimal weight:   10.0000
   chunk 57 optimal weight:    2.9990
   chunk 60 optimal weight:    6.9990
   chunk 51 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.055480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.041048 restraints weight = 20092.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.2822 rms_B_bonded: 4.73
r_work: 0.2675 rms_B_bonded: 4.98 restraints_weight: 0.5000
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.2190

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= 0.140
  Angle     :  0.639  13.028   7189  Z= 0.304
  Chirality :  0.043   0.259    804
  Planarity :  0.003   0.041    928
  Dihedral  :  4.535  20.890    717
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 12.61 %
    Favored  : 85.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.33), residues: 646
  helix:  2.35 (0.41), residues: 156
  sheet: -0.10 (0.37), residues: 203
  loop : -1.42 (0.34), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 349 
 TYR   0.012   0.001   TYR A 203 
 PHE   0.008   0.001   PHE B 225 
 TRP   0.011   0.001   TRP B 407 
 HIS   0.006   0.001   HIS B 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 5305)
  covalent geometry    : angle       0.63909 ( 7189)
  hydrogen bonds       : bond        0.03276 (  150)
  hydrogen bonds       : angle       4.47506 (  438)

********************** 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
  53 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A  152 MET cc_start: 0.7761 (ptt) cc_final: 0.6434 (pmm)
REVERT: A  216 ASN cc_start: 0.9267 (m110) cc_final: 0.9048 (p0)
REVERT: A  224 TYR cc_start: 0.8875 (t80) cc_final: 0.8567 (t80)
REVERT: B  219 MET cc_start: 0.8694 (tmm) cc_final: 0.8215 (tmm)
REVERT: B  237 MET cc_start: 0.8808 (mmm) cc_final: 0.8466 (mmm)
REVERT: B  315 ARG cc_start: 0.9350 (ttt90) cc_final: 0.8891 (ttm110)
  outliers start: 12
  outliers final: 10
  residues processed: 48
  average time/residue: 0.0790
  time to fit residues: 5.0872
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  : 0.207 
-------------------------------------------------------------------------------
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  156 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 56 optimal weight:    9.9990
   chunk 61 optimal weight:    0.3980
   chunk 13 optimal weight:   10.0000
   chunk 6 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0270
   chunk 1 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   overall best weight:    1.4642

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.055298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.040687 restraints weight = 20475.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.2810 rms_B_bonded: 4.79
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.2279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5305  Z= 0.165
  Angle     :  0.660  11.725   7189  Z= 0.322
  Chirality :  0.044   0.278    804
  Planarity :  0.004   0.045    928
  Dihedral  :  4.592  21.380    717
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.32 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.33), residues: 646
  helix:  2.20 (0.41), residues: 156
  sheet: -0.34 (0.36), residues: 218
  loop : -1.28 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 349 
 TYR   0.012   0.001   TYR A 203 
 PHE   0.011   0.001   PHE B 321 
 TRP   0.011   0.001   TRP B 407 
 HIS   0.006   0.001   HIS B 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 5305)
  covalent geometry    : angle       0.65955 ( 7189)
  hydrogen bonds       : bond        0.03441 (  150)
  hydrogen bonds       : angle       4.53510 (  438)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1267.98 seconds
wall clock time: 22 minutes 23.87 seconds (1343.87 seconds total)