Starting phenix.real_space_refine
on Sat May 10 04:44:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yoy_39460/05_2025/8yoy_39460.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yoy_39460/05_2025/8yoy_39460.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.21
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yoy_39460/05_2025/8yoy_39460.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yoy_39460/05_2025/8yoy_39460.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yoy_39460/05_2025/8yoy_39460.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yoy_39460/05_2025/8yoy_39460.cif"
  }
  resolution = 3.21
  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=   0.018
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      47      5.16       5
     C    3185      2.51       5
     N     879      2.21       5
     O     970      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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5081
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2248
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2248
          Classifications: {'peptide': 289}
          Link IDs: {'PTRANS': 14, 'TRANS': 274}
    Chain: "B"
      Number of atoms: 2833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 364, 2833
          Classifications: {'peptide': 364}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 346}
  Time building chain proxies: 3.62, per 1000 atoms: 0.71
  Number of scatterers: 5081
  At special positions: 0
  Unit cell: (63.99, 78.57, 136.89, 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      47     16.00
     O     970      8.00
     N     879      7.00
     C    3185      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=17, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 327 " - pdb=" SG  CYS A 352 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 370 " - pdb=" SG  CYS A 423 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 382 " - pdb=" SG  CYS A 605 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 466 " - pdb=" SG  CYS A 546 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 474 " - pdb=" SG  CYS A 495 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 476 " - pdb=" SG  CYS A 567 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 485 " - pdb=" SG  CYS A 516 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 504 " - pdb=" SG  CYS A 518 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 520 " - pdb=" SG  CYS A 533 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 556 " - pdb=" SG  CYS A 569 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 133 " - pdb=" SG  CYS B 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 172 " - pdb=" SG  CYS B 231 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 185 " - pdb=" SG  CYS B 241 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 244 " - pdb=" SG  CYS B 365 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 281 " - pdb=" SG  CYS B 297 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 410 " - pdb=" SG  CYS B 426 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 437 " - pdb=" SG  CYS B 465 " distance=2.03

  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: 1.11
  Conformation dependent library (CDL) restraints added in 728.0 milliseconds
  

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1212

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 10 sheets defined
      15.0% alpha, 22.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 328 through 334
      removed outlier: 3.654A  pdb=" N   TRP A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 344
      removed outlier: 3.915A  pdb=" N   TRP A 344 " --> pdb=" O   PRO A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 363
    Processing helix  chain 'A' and resid 397 through 402
      removed outlier: 3.877A  pdb=" N   GLN A 402 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 413
    Processing helix  chain 'A' and resid 442 through 448
      removed outlier: 3.581A  pdb=" N   ARG A 446 " --> pdb=" O   SER A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 483
    Processing helix  chain 'A' and resid 552 through 556
      removed outlier: 3.727A  pdb=" N   LYS A 555 " --> pdb=" O   ASP A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 574
    Processing helix  chain 'B' and resid 142 through 147
    Processing helix  chain 'B' and resid 177 through 188
      removed outlier: 3.786A  pdb=" N   GLY B 181 " --> pdb=" O   ASN B 177 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ALA B 183 " --> pdb=" O   ASN B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 298
      removed outlier: 3.540A  pdb=" N   CYS B 297 " --> pdb=" O   ALA B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 411
    Processing helix  chain 'B' and resid 480 through 491
      removed outlier: 3.590A  pdb=" N   ALA B 490 " --> pdb=" O   ARG B 486 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 337 through 338
    Processing sheet with id=AA2, first strand: chain 'A' and resid 345 through 349
      removed outlier: 3.584A  pdb=" N   GLU A 345 " --> pdb=" O   LYS A 390 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LYS A 390 " --> pdb=" O   GLU A 345 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   SER A 385 " --> pdb=" O   ASN A 597 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   SER A 367 " --> pdb=" O   TYR A 426 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   SER A 428 " --> pdb=" O   THR A 365 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   THR A 365 " --> pdb=" O   SER A 428 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 459 through 463
    Processing sheet with id=AA4, first strand: chain 'A' and resid 466 through 468
      removed outlier: 4.521A  pdb=" N   CYS A 466 " --> pdb=" O   SER A 538 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LYS A 536 " --> pdb=" O   SER A 468 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 504 through 507
    Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 150
    Processing sheet with id=AA7, first strand: chain 'B' and resid 196 through 200
    Processing sheet with id=AA8, first strand: chain 'B' and resid 209 through 211
    Processing sheet with id=AA9, first strand: chain 'B' and resid 270 through 275
      removed outlier: 3.773A  pdb=" N   CYS B 281 " --> pdb=" O   LEU B 273 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   VAL B 275 " --> pdb=" O   HIS B 279 " (cutoff:3.500A)
      removed outlier: 5.344A  pdb=" N   HIS B 279 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   LEU B 348 " --> pdb=" O   VAL B 331 " (cutoff:3.500A)
      removed outlier: 4.768A  pdb=" N   VAL B 331 " --> pdb=" O   LEU B 348 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   LYS B 350 " --> pdb=" O   GLU B 329 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   VAL B 328 " --> pdb=" O   TRP B 308 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   TRP B 308 " --> pdb=" O   VAL B 328 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 378 through 383
      removed outlier: 4.246A  pdb=" N   CYS B 426 " --> pdb=" O   ILE B 405 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   VAL B 473 " --> pdb=" O   SER B 460 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   THR B 447 " --> pdb=" O   TRP B 454 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   LEU B 445 " --> pdb=" O   ILE B 456 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   SER B 382 " --> pdb=" O   PRO B 444 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   SER B 448 " --> pdb=" O   LEU B 378 " (cutoff:3.500A)
      removed outlier: 7.278A  pdb=" N   LEU B 378 " --> pdb=" O   SER B 448 " (cutoff:3.500A)

    125 hydrogen bonds defined for protein.
    318 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: 1.62

  Time building geometry restraints manager: 1.39 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1665
        1.34 -     1.46: 1156
        1.46 -     1.58: 2339
        1.58 -     1.69: 0
        1.69 -     1.81: 56
  Bond restraints: 5216
  Sorted by residual:
  bond pdb=" CA  ASN A 351 "
       pdb=" CB  ASN A 351 "
    ideal  model  delta    sigma   weight residual
    1.530  1.543 -0.012 1.69e-02 3.50e+03 5.39e-01
  bond pdb=" C   PRO A 325 "
       pdb=" O   PRO A 325 "
    ideal  model  delta    sigma   weight residual
    1.235  1.227  0.008 1.30e-02 5.92e+03 4.08e-01
  bond pdb=" CA  PRO A 339 "
       pdb=" C   PRO A 339 "
    ideal  model  delta    sigma   weight residual
    1.526  1.519  0.007 1.13e-02 7.83e+03 3.40e-01
  bond pdb=" CD1 TYR B 414 "
       pdb=" CE1 TYR B 414 "
    ideal  model  delta    sigma   weight residual
    1.382  1.365  0.017 3.00e-02 1.11e+03 3.37e-01
  bond pdb=" CB  TYR B 414 "
       pdb=" CG  TYR B 414 "
    ideal  model  delta    sigma   weight residual
    1.512  1.500  0.012 2.20e-02 2.07e+03 3.14e-01
  ... (remaining 5211 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.12: 6855
        1.12 -     2.24: 179
        2.24 -     3.35: 46
        3.35 -     4.47: 10
        4.47 -     5.59: 4
  Bond angle restraints: 7094
  Sorted by residual:
  angle pdb=" C   SER A 350 "
        pdb=" N   ASN A 351 "
        pdb=" CA  ASN A 351 "
      ideal   model   delta    sigma   weight residual
     121.54  127.13   -5.59 1.91e+00 2.74e-01 8.56e+00
  angle pdb=" C   ALA B 468 "
        pdb=" N   TYR B 469 "
        pdb=" CA  TYR B 469 "
      ideal   model   delta    sigma   weight residual
     121.54  126.84   -5.30 1.91e+00 2.74e-01 7.70e+00
  angle pdb=" C   GLY B 432 "
        pdb=" N   ASN B 433 "
        pdb=" CA  ASN B 433 "
      ideal   model   delta    sigma   weight residual
     121.54  125.94   -4.40 1.91e+00 2.74e-01 5.30e+00
  angle pdb=" C   ASN A 585 "
        pdb=" N   ASN A 586 "
        pdb=" CA  ASN A 586 "
      ideal   model   delta    sigma   weight residual
     121.54  125.24   -3.70 1.91e+00 2.74e-01 3.75e+00
  angle pdb=" C   ILE B 256 "
        pdb=" N   VAL B 257 "
        pdb=" CA  VAL B 257 "
      ideal   model   delta    sigma   weight residual
     121.97  125.28   -3.31 1.80e+00 3.09e-01 3.38e+00
  ... (remaining 7089 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.00: 2708
       16.00 -    32.00: 314
       32.00 -    47.99: 82
       47.99 -    63.99: 13
       63.99 -    79.99: 5
  Dihedral angle restraints: 3122
    sinusoidal: 1232
      harmonic: 1890
  Sorted by residual:
  dihedral pdb=" CB  CYS A 474 "
           pdb=" SG  CYS A 474 "
           pdb=" SG  CYS A 495 "
           pdb=" CB  CYS A 495 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.04  -73.04     1      1.00e+01 1.00e-02 6.80e+01
  dihedral pdb=" CB  CYS B 133 "
           pdb=" SG  CYS B 133 "
           pdb=" SG  CYS B 148 "
           pdb=" CB  CYS B 148 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -141.43   55.43     1      1.00e+01 1.00e-02 4.15e+01
  dihedral pdb=" CB  CYS A 520 "
           pdb=" SG  CYS A 520 "
           pdb=" SG  CYS A 533 "
           pdb=" CB  CYS A 533 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.92  -41.92     1      1.00e+01 1.00e-02 2.46e+01
  ... (remaining 3119 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 443
       0.029 -    0.059: 178
       0.059 -    0.088: 88
       0.088 -    0.118: 41
       0.118 -    0.147: 5
  Chirality restraints: 755
  Sorted by residual:
  chirality pdb=" CA  ASN A 351 "
            pdb=" N   ASN A 351 "
            pdb=" C   ASN A 351 "
            pdb=" CB  ASN A 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.43e-01
  chirality pdb=" CG  LEU A 333 "
            pdb=" CB  LEU A 333 "
            pdb=" CD1 LEU A 333 "
            pdb=" CD2 LEU A 333 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 4.58e-01
  chirality pdb=" CA  ILE B 291 "
            pdb=" N   ILE B 291 "
            pdb=" C   ILE B 291 "
            pdb=" CB  ILE B 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.50e-01
  ... (remaining 752 not shown)

  Planarity restraints: 923
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 421 "   -0.029 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO B 422 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 422 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 422 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 287 "    0.023 5.00e-02 4.00e+02   3.45e-02 1.90e+00
        pdb=" N   PRO B 288 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO B 288 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 288 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 393 "   -0.019 5.00e-02 4.00e+02   2.81e-02 1.27e+00
        pdb=" N   PRO A 394 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A 394 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 394 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 920 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 302
        2.73 -     3.27: 5113
        3.27 -     3.82: 8499
        3.82 -     4.36: 10021
        4.36 -     4.90: 16859
  Nonbonded interactions: 40794
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 496 "
            pdb=" OG1 THR A 499 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" OE1 GLU B 178 "
            pdb=" OG  SER B 197 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OG  SER A 340 "
            pdb=" OD1 ASN A 343 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OG  SER A 562 "
            pdb=" OD1 ASN A 564 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OE2 GLU B 299 "
            pdb=" OH  TYR B 337 "
     model   vdw
     2.291 3.040
  ... (remaining 40789 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=0.83 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.930
  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:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     17.380
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:4.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4445
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   0.021   5233  Z= 0.152
  Angle     :  0.501   5.588   7128  Z= 0.269
  Chirality :  0.043   0.147    755
  Planarity :  0.004   0.045    923
  Dihedral  : 14.417  79.990   1859
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 16.00 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.32), residues: 649
  helix: -2.36 (0.45), residues: 81
  sheet: -0.27 (0.42), residues: 175
  loop : -0.82 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 515 
 HIS   0.003   0.000   HIS B 296 
 PHE   0.005   0.001   PHE A 391 
 TYR   0.008   0.001   TYR B 222 
 ARG   0.003   0.000   ARG B 409 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27225 (  125)
  hydrogen bonds       : angle      10.42553 (  318)
  SS BOND              : bond        0.00384 (   17)
  SS BOND              : angle       0.55331 (   34)
  covalent geometry    : bond        0.00344 ( 5216)
  covalent geometry    : angle       0.50041 ( 7094)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.1847
  time to fit residues: 34.3869
Evaluate side-chains
  71 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 48 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.3980
   chunk 37 optimal weight:    0.0070
   chunk 58 optimal weight:    6.9990
   overall best weight:    1.4804

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

Flipped N/Q/H residues before XYZ refinement:
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 450 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.102783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.087499 restraints weight = 20274.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.4129 rms_B_bonded: 7.01
r_work (final): 0.4129
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4130
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4130 r_free = 0.4130    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4131 r_free = 0.4131    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4131
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.3842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5233  Z= 0.195
  Angle     :  0.676   8.795   7128  Z= 0.364
  Chirality :  0.049   0.174    755
  Planarity :  0.005   0.053    923
  Dihedral  :  4.731  18.919    704
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 16.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 19.65 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.32), residues: 649
  helix: -1.95 (0.52), residues: 77
  sheet: -0.82 (0.40), residues: 175
  loop : -0.59 (0.31), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP B 168 
 HIS   0.009   0.002   HIS B 279 
 PHE   0.023   0.003   PHE B 311 
 TYR   0.010   0.002   TYR B 474 
 ARG   0.005   0.001   ARG B 409 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04574 (  125)
  hydrogen bonds       : angle       7.87648 (  318)
  SS BOND              : bond        0.00476 (   17)
  SS BOND              : angle       0.95776 (   34)
  covalent geometry    : bond        0.00412 ( 5216)
  covalent geometry    : angle       0.67396 ( 7094)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8817 (pp)
REVERT: A  345 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7575 (mt-10)
REVERT: A  437 ASN cc_start: 0.9262 (OUTLIER) cc_final: 0.9049 (p0)
REVERT: A  589 ASN cc_start: 0.7945 (t0) cc_final: 0.7507 (p0)
REVERT: A  604 THR cc_start: 0.5700 (OUTLIER) cc_final: 0.5450 (t)
REVERT: B  132 TRP cc_start: 0.5462 (t-100) cc_final: 0.5201 (t-100)
REVERT: B  178 GLU cc_start: 0.9267 (tt0) cc_final: 0.8919 (tt0)
REVERT: B  188 MET cc_start: 0.7874 (mtt) cc_final: 0.7021 (mtp)
REVERT: B  202 ASP cc_start: 0.8351 (p0) cc_final: 0.8092 (p0)
REVERT: B  239 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7651 (tp)
REVERT: B  317 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8032 (mm-40)
REVERT: B  371 MET cc_start: 0.6359 (ptp) cc_final: 0.5927 (ptp)
REVERT: B  395 GLU cc_start: 0.8834 (tp30) cc_final: 0.8518 (tp30)
REVERT: B  417 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8224 (m-30)
REVERT: B  454 TRP cc_start: 0.7626 (m100) cc_final: 0.6927 (m100)
  outliers start: 16
  outliers final: 4
  residues processed: 94
  average time/residue: 0.1948
  time to fit residues: 23.3585
Evaluate side-chains
  67 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  437 ASN
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  417 ASP
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  479 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 59 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 51 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 353 ASN
A 535 GLN
** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 193 ASN
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 317 GLN
** B 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.093329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.078842 restraints weight = 22679.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3948 rms_B_bonded: 6.82
r_work (final): 0.3948
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3950
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3950 r_free = 0.3950    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3949 r_free = 0.3949    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3949
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.5549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   5233  Z= 0.244
  Angle     :  0.725  11.204   7128  Z= 0.385
  Chirality :  0.050   0.218    755
  Planarity :  0.005   0.049    923
  Dihedral  :  5.280  23.157    704
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 25.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 18.78 %
    Favored  : 76.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.31), residues: 649
  helix: -1.54 (0.59), residues: 64
  sheet: -1.21 (0.39), residues: 171
  loop : -0.82 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP B 380 
 HIS   0.005   0.002   HIS B 279 
 PHE   0.029   0.003   PHE A 373 
 TYR   0.015   0.002   TYR B 222 
 ARG   0.018   0.001   ARG B 409 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05223 (  125)
  hydrogen bonds       : angle       7.33852 (  318)
  SS BOND              : bond        0.00264 (   17)
  SS BOND              : angle       1.00362 (   34)
  covalent geometry    : bond        0.00527 ( 5216)
  covalent geometry    : angle       0.72334 ( 7094)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 69
  time to evaluate  : 0.624 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9108 (pp)
REVERT: A  345 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7504 (mt-10)
REVERT: A  589 ASN cc_start: 0.8199 (t0) cc_final: 0.7886 (p0)
REVERT: B  188 MET cc_start: 0.7830 (mtt) cc_final: 0.7344 (mmt)
REVERT: B  200 ILE cc_start: 0.9017 (pt) cc_final: 0.8571 (mm)
REVERT: B  202 ASP cc_start: 0.8635 (p0) cc_final: 0.7689 (t0)
REVERT: B  317 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8072 (tp-100)
REVERT: B  320 MET cc_start: 0.7997 (ptp) cc_final: 0.7414 (ptp)
REVERT: B  334 HIS cc_start: 0.9113 (t-90) cc_final: 0.8378 (t-90)
REVERT: B  371 MET cc_start: 0.7129 (ptp) cc_final: 0.6877 (ptp)
REVERT: B  417 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8482 (m-30)
  outliers start: 29
  outliers final: 15
  residues processed: 89
  average time/residue: 0.1543
  time to fit residues: 18.2652
Evaluate side-chains
  80 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  353 ASN
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  597 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain B residue  317 GLN
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  407 THR
Chi-restraints excluded: chain B residue  410 CYS
Chi-restraints excluded: chain B residue  417 ASP
Chi-restraints excluded: chain B residue  429 PHE
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  478 MET
Chi-restraints excluded: chain B residue  479 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 45 optimal weight:    0.0980
   chunk 54 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 36 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 353 ASN
A 535 GLN
B 198 GLN
** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.096787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.081579 restraints weight = 22601.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.4009 rms_B_bonded: 7.15
r_work (final): 0.4009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.5638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5233  Z= 0.128
  Angle     :  0.623   6.460   7128  Z= 0.323
  Chirality :  0.047   0.207    755
  Planarity :  0.004   0.040    923
  Dihedral  :  4.857  19.830    704
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 18.01
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.39 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 21.91 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.31), residues: 649
  helix: -1.21 (0.61), residues: 65
  sheet: -1.30 (0.36), residues: 180
  loop : -0.72 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B 380 
 HIS   0.005   0.001   HIS B 274 
 PHE   0.016   0.002   PHE A 481 
 TYR   0.012   0.002   TYR A 465 
 ARG   0.006   0.001   ARG B 409 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03728 (  125)
  hydrogen bonds       : angle       6.77587 (  318)
  SS BOND              : bond        0.00175 (   17)
  SS BOND              : angle       0.76245 (   34)
  covalent geometry    : bond        0.00291 ( 5216)
  covalent geometry    : angle       0.62233 ( 7094)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8887 (pp)
REVERT: A  345 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7547 (mt-10)
REVERT: A  353 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8454 (p0)
REVERT: A  537 LYS cc_start: 0.8345 (tptt) cc_final: 0.8020 (tptp)
REVERT: B  188 MET cc_start: 0.7775 (mtt) cc_final: 0.7236 (mmt)
REVERT: B  202 ASP cc_start: 0.8433 (p0) cc_final: 0.7493 (t0)
REVERT: B  269 TRP cc_start: 0.8385 (p90) cc_final: 0.7990 (p90)
REVERT: B  317 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8391 (tp-100)
REVERT: B  320 MET cc_start: 0.8046 (ptp) cc_final: 0.7013 (ptp)
REVERT: B  334 HIS cc_start: 0.9067 (t-90) cc_final: 0.8389 (t-90)
REVERT: B  359 ASP cc_start: 0.9613 (m-30) cc_final: 0.9171 (p0)
REVERT: B  417 ASP cc_start: 0.8964 (OUTLIER) cc_final: 0.8434 (m-30)
  outliers start: 20
  outliers final: 9
  residues processed: 84
  average time/residue: 0.1653
  time to fit residues: 18.2161
Evaluate side-chains
  77 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  353 ASN
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  317 GLN
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  407 THR
Chi-restraints excluded: chain B residue  410 CYS
Chi-restraints excluded: chain B residue  415 VAL
Chi-restraints excluded: chain B residue  417 ASP
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  479 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 61 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 47 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 353 ASN
A 535 GLN
** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 433 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.094338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.078507 restraints weight = 22336.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3958 rms_B_bonded: 7.22
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.6194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5233  Z= 0.163
  Angle     :  0.633   6.683   7128  Z= 0.329
  Chirality :  0.047   0.179    755
  Planarity :  0.004   0.039    923
  Dihedral  :  4.876  22.346    704
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 20.95
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.55 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 21.74 %
    Favored  : 73.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.32), residues: 649
  helix: -1.13 (0.61), residues: 71
  sheet: -1.40 (0.37), residues: 177
  loop : -0.67 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 380 
 HIS   0.005   0.001   HIS B 274 
 PHE   0.016   0.002   PHE B 311 
 TYR   0.012   0.002   TYR B 222 
 ARG   0.006   0.001   ARG B 409 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03748 (  125)
  hydrogen bonds       : angle       6.91711 (  318)
  SS BOND              : bond        0.00211 (   17)
  SS BOND              : angle       0.76737 (   34)
  covalent geometry    : bond        0.00354 ( 5216)
  covalent geometry    : angle       0.63233 ( 7094)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 73
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8928 (pp)
REVERT: A  345 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7563 (mt-10)
REVERT: A  353 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8465 (p0)
REVERT: A  446 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8327 (ptt-90)
REVERT: A  501 TYR cc_start: 0.7601 (OUTLIER) cc_final: 0.7228 (t80)
REVERT: B  188 MET cc_start: 0.7751 (mtt) cc_final: 0.6707 (mtp)
REVERT: B  202 ASP cc_start: 0.8568 (p0) cc_final: 0.7677 (t0)
REVERT: B  269 TRP cc_start: 0.8334 (p90) cc_final: 0.8111 (p90)
REVERT: B  334 HIS cc_start: 0.9184 (t-90) cc_final: 0.8357 (t-90)
REVERT: B  362 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8919 (mptt)
REVERT: B  371 MET cc_start: 0.7127 (ptp) cc_final: 0.6853 (ptp)
REVERT: B  395 GLU cc_start: 0.8890 (tp30) cc_final: 0.8515 (tp30)
REVERT: B  401 LYS cc_start: 0.8740 (tttm) cc_final: 0.8440 (tmtt)
REVERT: B  417 ASP cc_start: 0.9112 (OUTLIER) cc_final: 0.8579 (m-30)
  outliers start: 27
  outliers final: 15
  residues processed: 91
  average time/residue: 0.1893
  time to fit residues: 21.8363
Evaluate side-chains
  89 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 68
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  353 ASN
Chi-restraints excluded: chain A residue  446 ARG
Chi-restraints excluded: chain A residue  458 HIS
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  488 HIS
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  213 ASN
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  362 LYS
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  410 CYS
Chi-restraints excluded: chain B residue  415 VAL
Chi-restraints excluded: chain B residue  417 ASP
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  478 MET
Chi-restraints excluded: chain B residue  479 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 44 optimal weight:    0.7980
   chunk 47 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 27 optimal weight:    8.9990
   chunk 6 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0870
   chunk 53 optimal weight:    0.0970
   chunk 58 optimal weight:    0.6980
   chunk 8 optimal weight:    5.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.4556

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

Flipped N/Q/H residues before XYZ refinement:
A 353 ASN
A 364 HIS
B 193 ASN
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 487 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.096661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.081858 restraints weight = 21676.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.4021 rms_B_bonded: 7.02
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.6187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   5233  Z= 0.114
  Angle     :  0.631   9.452   7128  Z= 0.322
  Chirality :  0.046   0.168    755
  Planarity :  0.004   0.037    923
  Dihedral  :  4.622  21.707    704
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.70 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 22.96 %
    Favored  : 72.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.32), residues: 649
  helix: -0.51 (0.69), residues: 59
  sheet: -1.27 (0.37), residues: 181
  loop : -0.49 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 380 
 HIS   0.004   0.001   HIS B 274 
 PHE   0.013   0.002   PHE B 311 
 TYR   0.010   0.001   TYR A 465 
 ARG   0.006   0.001   ARG B 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03153 (  125)
  hydrogen bonds       : angle       6.63674 (  318)
  SS BOND              : bond        0.00158 (   17)
  SS BOND              : angle       0.67258 (   34)
  covalent geometry    : bond        0.00258 ( 5216)
  covalent geometry    : angle       0.63038 ( 7094)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 74
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8803 (pp)
REVERT: A  345 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7529 (mt-10)
REVERT: A  353 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8551 (p0)
REVERT: A  363 VAL cc_start: 0.9029 (OUTLIER) cc_final: 0.8817 (p)
REVERT: A  446 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8175 (ptt180)
REVERT: A  501 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.7246 (t80)
REVERT: A  610 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8693 (pt)
REVERT: B  188 MET cc_start: 0.7752 (mtt) cc_final: 0.6598 (mtp)
REVERT: B  202 ASP cc_start: 0.8390 (p0) cc_final: 0.7472 (t0)
REVERT: B  269 TRP cc_start: 0.8475 (p90) cc_final: 0.8017 (p90)
REVERT: B  334 HIS cc_start: 0.9060 (t-90) cc_final: 0.8270 (t-90)
REVERT: B  362 LYS cc_start: 0.9156 (mttm) cc_final: 0.8681 (mtmm)
REVERT: B  371 MET cc_start: 0.6993 (ptp) cc_final: 0.6718 (ptp)
REVERT: B  401 LYS cc_start: 0.8650 (tttm) cc_final: 0.8412 (tmtt)
REVERT: B  417 ASP cc_start: 0.9025 (OUTLIER) cc_final: 0.8488 (m-30)
REVERT: B  488 MET cc_start: 0.6796 (mtp) cc_final: 0.6404 (mtp)
REVERT: B  491 ASP cc_start: 0.7633 (m-30) cc_final: 0.7426 (m-30)
  outliers start: 24
  outliers final: 12
  residues processed: 93
  average time/residue: 0.1872
  time to fit residues: 22.1222
Evaluate side-chains
  86 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  353 ASN
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  437 ASN
Chi-restraints excluded: chain A residue  446 ARG
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  213 ASN
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  410 CYS
Chi-restraints excluded: chain B residue  415 VAL
Chi-restraints excluded: chain B residue  417 ASP
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  478 MET
Chi-restraints excluded: chain B residue  479 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 45 optimal weight:    0.0470
   chunk 3 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 51 optimal weight:    7.9990
   chunk 26 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    1.2680

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

Flipped N/Q/H residues before XYZ refinement:
A 353 ASN
A 364 HIS
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.095014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.080180 restraints weight = 22585.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3979 rms_B_bonded: 6.95
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.6506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   5233  Z= 0.154
  Angle     :  0.640   7.394   7128  Z= 0.330
  Chirality :  0.047   0.192    755
  Planarity :  0.004   0.040    923
  Dihedral  :  4.764  21.539    704
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 19.23
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.62 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 23.13 %
    Favored  : 72.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.33), residues: 649
  helix: -0.37 (0.72), residues: 59
  sheet: -1.26 (0.37), residues: 179
  loop : -0.55 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 380 
 HIS   0.004   0.001   HIS B 274 
 PHE   0.018   0.002   PHE B 311 
 TYR   0.014   0.002   TYR B 414 
 ARG   0.006   0.001   ARG B 409 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03509 (  125)
  hydrogen bonds       : angle       6.54386 (  318)
  SS BOND              : bond        0.00191 (   17)
  SS BOND              : angle       0.73786 (   34)
  covalent geometry    : bond        0.00353 ( 5216)
  covalent geometry    : angle       0.63922 ( 7094)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 74
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8960 (pp)
REVERT: A  345 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7520 (mt-10)
REVERT: A  501 TYR cc_start: 0.7760 (OUTLIER) cc_final: 0.7316 (t80)
REVERT: A  537 LYS cc_start: 0.8224 (tptt) cc_final: 0.7901 (tptp)
REVERT: A  610 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8734 (pt)
REVERT: B  178 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8746 (tp30)
REVERT: B  188 MET cc_start: 0.7696 (mtt) cc_final: 0.6600 (mtp)
REVERT: B  202 ASP cc_start: 0.8432 (p0) cc_final: 0.7541 (t0)
REVERT: B  269 TRP cc_start: 0.8434 (p90) cc_final: 0.7995 (p90)
REVERT: B  334 HIS cc_start: 0.9122 (t-90) cc_final: 0.8599 (t-90)
REVERT: B  362 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8730 (mtmm)
REVERT: B  371 MET cc_start: 0.7136 (ptp) cc_final: 0.6905 (ptp)
REVERT: B  401 LYS cc_start: 0.8623 (tttm) cc_final: 0.8419 (tmtt)
REVERT: B  417 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8517 (m-30)
  outliers start: 27
  outliers final: 20
  residues processed: 94
  average time/residue: 0.1721
  time to fit residues: 20.8097
Evaluate side-chains
  93 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 68
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  353 ASN
Chi-restraints excluded: chain A residue  437 ASN
Chi-restraints excluded: chain A residue  446 ARG
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  560 ASP
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  213 ASN
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  362 LYS
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  410 CYS
Chi-restraints excluded: chain B residue  415 VAL
Chi-restraints excluded: chain B residue  417 ASP
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  478 MET
Chi-restraints excluded: chain B residue  479 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 43 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 32 optimal weight:    0.1980
   chunk 17 optimal weight:    6.9990
   chunk 62 optimal weight:    0.6980
   chunk 11 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 353 ASN
A 364 HIS
** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.095391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.080566 restraints weight = 22516.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3997 rms_B_bonded: 6.94
r_work (final): 0.3997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.6668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   5233  Z= 0.140
  Angle     :  0.651   8.319   7128  Z= 0.333
  Chirality :  0.047   0.187    755
  Planarity :  0.004   0.037    923
  Dihedral  :  4.747  20.975    704
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 19.33
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.31 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 23.83 %
    Favored  : 72.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.33), residues: 649
  helix: -0.35 (0.73), residues: 59
  sheet: -1.25 (0.38), residues: 179
  loop : -0.52 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 380 
 HIS   0.005   0.001   HIS B 274 
 PHE   0.021   0.002   PHE B 311 
 TYR   0.017   0.002   TYR B 414 
 ARG   0.008   0.001   ARG A 464 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03292 (  125)
  hydrogen bonds       : angle       6.46932 (  318)
  SS BOND              : bond        0.00170 (   17)
  SS BOND              : angle       0.71040 (   34)
  covalent geometry    : bond        0.00319 ( 5216)
  covalent geometry    : angle       0.65042 ( 7094)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 73
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8933 (pp)
REVERT: A  345 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7487 (mt-10)
REVERT: A  501 TYR cc_start: 0.7759 (OUTLIER) cc_final: 0.7276 (t80)
REVERT: A  537 LYS cc_start: 0.8280 (tptt) cc_final: 0.7985 (tptp)
REVERT: A  610 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8758 (pt)
REVERT: B  178 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8756 (tp30)
REVERT: B  188 MET cc_start: 0.7727 (mtt) cc_final: 0.6600 (mtp)
REVERT: B  202 ASP cc_start: 0.8413 (p0) cc_final: 0.7484 (t0)
REVERT: B  210 MET cc_start: 0.7666 (tpp) cc_final: 0.7365 (tpp)
REVERT: B  269 TRP cc_start: 0.8476 (p90) cc_final: 0.7991 (p90)
REVERT: B  289 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8038 (mm-30)
REVERT: B  334 HIS cc_start: 0.9130 (t-90) cc_final: 0.8607 (t-90)
REVERT: B  362 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8693 (mtmm)
REVERT: B  371 MET cc_start: 0.7079 (ptp) cc_final: 0.6847 (ptp)
REVERT: B  401 LYS cc_start: 0.8604 (tttm) cc_final: 0.8360 (tttm)
REVERT: B  417 ASP cc_start: 0.8935 (OUTLIER) cc_final: 0.8503 (m-30)
  outliers start: 24
  outliers final: 18
  residues processed: 91
  average time/residue: 0.1729
  time to fit residues: 20.6032
Evaluate side-chains
  92 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  353 ASN
Chi-restraints excluded: chain A residue  437 ASN
Chi-restraints excluded: chain A residue  446 ARG
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  560 ASP
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  213 ASN
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  362 LYS
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  410 CYS
Chi-restraints excluded: chain B residue  415 VAL
Chi-restraints excluded: chain B residue  417 ASP
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  478 MET
Chi-restraints excluded: chain B residue  479 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 55 optimal weight:    8.9990
   chunk 32 optimal weight:    0.0870
   chunk 26 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    1.1962

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

Flipped N/Q/H residues before XYZ refinement:
A 364 HIS
** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 159 GLN
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.093604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.078569 restraints weight = 22087.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.3974 rms_B_bonded: 6.95
r_work (final): 0.3974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.6895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   5233  Z= 0.149
  Angle     :  0.648   7.420   7128  Z= 0.332
  Chirality :  0.047   0.187    755
  Planarity :  0.004   0.037    923
  Dihedral  :  4.832  21.840    704
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 19.63
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.08 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 23.83 %
    Favored  : 71.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.33), residues: 649
  helix: -0.31 (0.73), residues: 59
  sheet: -1.33 (0.38), residues: 177
  loop : -0.63 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 380 
 HIS   0.004   0.001   HIS B 274 
 PHE   0.017   0.002   PHE B 311 
 TYR   0.016   0.002   TYR B 414 
 ARG   0.003   0.001   ARG A 464 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03403 (  125)
  hydrogen bonds       : angle       6.40870 (  318)
  SS BOND              : bond        0.00190 (   17)
  SS BOND              : angle       0.70943 (   34)
  covalent geometry    : bond        0.00335 ( 5216)
  covalent geometry    : angle       0.64734 ( 7094)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 74
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8956 (pp)
REVERT: A  446 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8284 (ptt-90)
REVERT: A  501 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.7251 (t80)
REVERT: A  537 LYS cc_start: 0.8247 (tptt) cc_final: 0.7967 (tptp)
REVERT: A  610 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8739 (pt)
REVERT: B  178 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8772 (tp30)
REVERT: B  188 MET cc_start: 0.7697 (mtt) cc_final: 0.6571 (mtp)
REVERT: B  202 ASP cc_start: 0.8439 (p0) cc_final: 0.7530 (t0)
REVERT: B  210 MET cc_start: 0.7757 (tpp) cc_final: 0.7428 (tpp)
REVERT: B  269 TRP cc_start: 0.8468 (p90) cc_final: 0.7996 (p90)
REVERT: B  289 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8154 (mm-30)
REVERT: B  334 HIS cc_start: 0.9173 (t-90) cc_final: 0.8654 (t-90)
REVERT: B  362 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8669 (mtmm)
REVERT: B  371 MET cc_start: 0.7114 (ptp) cc_final: 0.6816 (ptp)
REVERT: B  401 LYS cc_start: 0.8607 (tttm) cc_final: 0.8346 (tttm)
REVERT: B  417 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8533 (m-30)
  outliers start: 26
  outliers final: 18
  residues processed: 94
  average time/residue: 0.1610
  time to fit residues: 19.8521
Evaluate side-chains
  91 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 67
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  353 ASN
Chi-restraints excluded: chain A residue  366 ASP
Chi-restraints excluded: chain A residue  446 ARG
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  560 ASP
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain A residue  597 ASN
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  213 ASN
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  362 LYS
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  410 CYS
Chi-restraints excluded: chain B residue  415 VAL
Chi-restraints excluded: chain B residue  417 ASP
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  478 MET
Chi-restraints excluded: chain B residue  479 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 52 optimal weight:    0.2980
   chunk 21 optimal weight:    0.5980
   chunk 22 optimal weight:   10.0000
   chunk 41 optimal weight:    0.0020
   chunk 33 optimal weight:    0.5980
   chunk 57 optimal weight:    0.7980
   chunk 24 optimal weight:    4.9990
   chunk 40 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   overall best weight:    0.4588

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

Flipped N/Q/H residues before XYZ refinement:
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 ASN ** 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 = 0.4327 r_free = 0.4327 target = 0.096106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.081283 restraints weight = 22043.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.4028 rms_B_bonded: 7.02
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.6882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5233  Z= 0.126
  Angle     :  0.688   8.956   7128  Z= 0.350
  Chirality :  0.047   0.179    755
  Planarity :  0.004   0.037    923
  Dihedral  :  4.749  25.594    704
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 16.29
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.08 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 25.04 %
    Favored  : 71.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.33), residues: 649
  helix: -0.25 (0.72), residues: 60
  sheet: -1.31 (0.38), residues: 171
  loop : -0.56 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 269 
 HIS   0.005   0.001   HIS B 274 
 PHE   0.020   0.002   PHE B 311 
 TYR   0.019   0.001   TYR A 465 
 ARG   0.003   0.001   ARG A 464 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03076 (  125)
  hydrogen bonds       : angle       6.21238 (  318)
  SS BOND              : bond        0.00145 (   17)
  SS BOND              : angle       0.61508 (   34)
  covalent geometry    : bond        0.00287 ( 5216)
  covalent geometry    : angle       0.68785 ( 7094)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 71
  time to evaluate  : 0.665 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8903 (pp)
REVERT: A  379 TYR cc_start: 0.8733 (m-80) cc_final: 0.8005 (m-80)
REVERT: A  501 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.7273 (t80)
REVERT: A  537 LYS cc_start: 0.8283 (tptt) cc_final: 0.8054 (tptp)
REVERT: A  610 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8755 (pt)
REVERT: B  178 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8773 (tp30)
REVERT: B  188 MET cc_start: 0.7662 (mtt) cc_final: 0.6600 (mtm)
REVERT: B  202 ASP cc_start: 0.8333 (p0) cc_final: 0.7402 (t0)
REVERT: B  210 MET cc_start: 0.7859 (tpp) cc_final: 0.7524 (tpp)
REVERT: B  269 TRP cc_start: 0.8467 (p90) cc_final: 0.7896 (p90)
REVERT: B  289 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8139 (mm-30)
REVERT: B  320 MET cc_start: 0.9238 (pmm) cc_final: 0.8946 (pmm)
REVERT: B  334 HIS cc_start: 0.9106 (t-90) cc_final: 0.8494 (t-90)
REVERT: B  362 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8524 (mtmm)
REVERT: B  371 MET cc_start: 0.7073 (ptp) cc_final: 0.6830 (ptp)
REVERT: B  401 LYS cc_start: 0.8567 (tttm) cc_final: 0.8367 (tttm)
REVERT: B  417 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8397 (m-30)
  outliers start: 22
  outliers final: 14
  residues processed: 90
  average time/residue: 0.1862
  time to fit residues: 21.5401
Evaluate side-chains
  87 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  366 ASP
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  446 ARG
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  213 ASN
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  362 LYS
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  410 CYS
Chi-restraints excluded: chain B residue  417 ASP
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  478 MET
Chi-restraints excluded: chain B residue  479 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 56 optimal weight:    0.2980
   chunk 53 optimal weight:    9.9990
   chunk 60 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 7 optimal weight:   10.0000
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 364 HIS
** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 193 ASN
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.093345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.078603 restraints weight = 22750.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3972 rms_B_bonded: 7.02
r_work (final): 0.3972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.7207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5233  Z= 0.155
  Angle     :  0.700   8.511   7128  Z= 0.359
  Chirality :  0.047   0.182    755
  Planarity :  0.004   0.037    923
  Dihedral  :  4.848  24.065    704
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 20.24
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.47 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 24.70 %
    Favored  : 71.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.33), residues: 649
  helix: -0.12 (0.75), residues: 58
  sheet: -1.44 (0.38), residues: 174
  loop : -0.56 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 380 
 HIS   0.006   0.001   HIS A 364 
 PHE   0.021   0.002   PHE B 311 
 TYR   0.013   0.002   TYR A 465 
 ARG   0.003   0.001   ARG A 531 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03354 (  125)
  hydrogen bonds       : angle       6.36171 (  318)
  SS BOND              : bond        0.00178 (   17)
  SS BOND              : angle       0.70289 (   34)
  covalent geometry    : bond        0.00346 ( 5216)
  covalent geometry    : angle       0.70011 ( 7094)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2952.12 seconds
wall clock time: 52 minutes 13.06 seconds (3133.06 seconds total)