Starting phenix.real_space_refine
on Sun Apr 27 08:09:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yoy_39460/04_2025/8yoy_39460.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yoy_39460/04_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_39460/04_2025/8yoy_39460.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yoy_39460/04_2025/8yoy_39460.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yoy_39460/04_2025/8yoy_39460.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yoy_39460/04_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-5669/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: 4.21, per 1000 atoms: 0.83
  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: 2.07
  Conformation dependent library (CDL) restraints added in 633.5 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: 0.67
  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: 1.45

  Time building geometry restraints manager: 2.35 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:             1.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.170
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.440
-------------------------------------------------------------------------------
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  : 0.610 
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: 0.2535
  time to fit residues: 47.4939
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  : 0.530 
-------------------------------------------------------------------------------
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 = 0.087492 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  : 0.599 
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: 0.8816 (pp)
REVERT: A  345 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7574 (mt-10)
REVERT: A  437 ASN cc_start: 0.9262 (OUTLIER) cc_final: 0.9049 (p0)
REVERT: A  589 ASN cc_start: 0.7946 (t0) cc_final: 0.7508 (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: 0.8920 (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: 0.7652 (tp)
REVERT: B  317 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8031 (mm-40)
REVERT: B  371 MET cc_start: 0.6358 (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: 0.8722 (OUTLIER) cc_final: 0.8224 (m-30)
REVERT: B  454 TRP cc_start: 0.7625 (m100) cc_final: 0.6927 (m100)
  outliers start: 16
  outliers final: 4
  residues processed: 94
  average time/residue: 0.1905
  time to fit residues: 22.6648
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  : 0.527 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 353 ASN
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 317 GLN
** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 398 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 = 0.4362 r_free = 0.4362 target = 0.099504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.084559 restraints weight = 22039.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.4073 rms_B_bonded: 7.05
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4073
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4073 r_free = 0.4073    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4071 r_free = 0.4071    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4071
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.4682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5233  Z= 0.158
  Angle     :  0.635  10.663   7128  Z= 0.332
  Chirality :  0.048   0.220    755
  Planarity :  0.004   0.047    923
  Dihedral  :  4.762  21.779    704
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 18.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 18.43 %
    Favored  : 77.22 %
  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: -1.32 (0.32), residues: 649
  helix: -1.68 (0.54), residues: 77
  sheet: -0.95 (0.40), residues: 175
  loop : -0.59 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 269 
 HIS   0.004   0.001   HIS A 512 
 PHE   0.027   0.002   PHE A 373 
 TYR   0.014   0.002   TYR A 465 
 ARG   0.013   0.001   ARG B 409 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04320 (  125)
  hydrogen bonds       : angle       7.02217 (  318)
  SS BOND              : bond        0.00200 (   17)
  SS BOND              : angle       0.72072 (   34)
  covalent geometry    : bond        0.00353 ( 5216)
  covalent geometry    : angle       0.63431 ( 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
  86 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 61
  time to evaluate  : 0.616 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8955 (pp)
REVERT: A  345 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7597 (mt-10)
REVERT: A  604 THR cc_start: 0.6046 (OUTLIER) cc_final: 0.5821 (t)
REVERT: B  178 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8871 (tt0)
REVERT: B  188 MET cc_start: 0.7804 (mtt) cc_final: 0.7290 (mmt)
REVERT: B  202 ASP cc_start: 0.8448 (p0) cc_final: 0.7491 (t0)
REVERT: B  317 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8387 (tp-100)
REVERT: B  320 MET cc_start: 0.8053 (ptp) cc_final: 0.7581 (ptp)
REVERT: B  362 LYS cc_start: 0.9228 (mttm) cc_final: 0.8743 (mttp)
REVERT: B  401 LYS cc_start: 0.8907 (mttt) cc_final: 0.8647 (pttp)
REVERT: B  417 ASP cc_start: 0.8909 (OUTLIER) cc_final: 0.8381 (m-30)
REVERT: B  454 TRP cc_start: 0.7797 (m100) cc_final: 0.7311 (m100)
  outliers start: 25
  outliers final: 11
  residues processed: 78
  average time/residue: 0.1943
  time to fit residues: 19.9137
Evaluate side-chains
  73 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
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 A residue  597 ASN
Chi-restraints excluded: chain A residue  604 THR
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  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  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:    0.0040
   chunk 54 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 24 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0770
   overall best weight:    0.9754

-------------------------------------------------------------------------------
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**
** B 398 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 = 0.4366 r_free = 0.4366 target = 0.099231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.083771 restraints weight = 22410.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.4069 rms_B_bonded: 7.23
r_work (final): 0.4069
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4070
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4070 r_free = 0.4070    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4070 r_free = 0.4070    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4070
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.5108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5233  Z= 0.134
  Angle     :  0.596   7.624   7128  Z= 0.314
  Chirality :  0.046   0.160    755
  Planarity :  0.004   0.040    923
  Dihedral  :  4.603  19.458    704
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 18.22
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.55 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 20.35 %
    Favored  : 76.35 %
  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: -1.24 (0.32), residues: 649
  helix: -1.11 (0.60), residues: 70
  sheet: -0.93 (0.40), residues: 173
  loop : -0.67 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 380 
 HIS   0.004   0.001   HIS B 274 
 PHE   0.016   0.002   PHE A 481 
 TYR   0.012   0.001   TYR A 465 
 ARG   0.007   0.001   ARG B 409 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03742 (  125)
  hydrogen bonds       : angle       6.75639 (  318)
  SS BOND              : bond        0.00196 (   17)
  SS BOND              : angle       0.71648 (   34)
  covalent geometry    : bond        0.00302 ( 5216)
  covalent geometry    : angle       0.59512 ( 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
  88 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.790 
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: 0.9165 (OUTLIER) cc_final: 0.8832 (pp)
REVERT: A  345 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7543 (mt-10)
REVERT: A  353 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8463 (p0)
REVERT: A  537 LYS cc_start: 0.8357 (tptt) cc_final: 0.8041 (tptp)
REVERT: A  604 THR cc_start: 0.6320 (OUTLIER) cc_final: 0.6098 (t)
REVERT: B  188 MET cc_start: 0.7746 (mtt) cc_final: 0.7202 (mmt)
REVERT: B  202 ASP cc_start: 0.8419 (p0) cc_final: 0.7479 (t0)
REVERT: B  320 MET cc_start: 0.8131 (ptp) cc_final: 0.6800 (ptp)
REVERT: B  332 ILE cc_start: 0.7853 (mm) cc_final: 0.7554 (mp)
REVERT: B  334 HIS cc_start: 0.8813 (t-90) cc_final: 0.8113 (t-90)
REVERT: B  359 ASP cc_start: 0.9626 (m-30) cc_final: 0.9196 (p0)
REVERT: B  362 LYS cc_start: 0.9225 (mttm) cc_final: 0.8721 (mttp)
REVERT: B  395 GLU cc_start: 0.9222 (tp30) cc_final: 0.8908 (tp30)
REVERT: B  401 LYS cc_start: 0.8973 (mttt) cc_final: 0.8684 (mptt)
REVERT: B  417 ASP cc_start: 0.8937 (OUTLIER) cc_final: 0.8429 (m-30)
  outliers start: 19
  outliers final: 10
  residues processed: 83
  average time/residue: 0.2777
  time to fit residues: 30.1579
Evaluate side-chains
  76 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
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 A residue  469 VAL
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain B residue  157 ILE
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 61 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 25 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
A 353 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.098696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.083562 restraints weight = 21682.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.4052 rms_B_bonded: 7.01
r_work (final): 0.4052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
moved from start:          0.5458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5233  Z= 0.125
  Angle     :  0.593   7.524   7128  Z= 0.309
  Chirality :  0.046   0.159    755
  Planarity :  0.004   0.038    923
  Dihedral  :  4.591  20.024    704
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 17.00
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.55 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 21.57 %
    Favored  : 74.78 %
  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: -1.04 (0.32), residues: 649
  helix: -0.55 (0.66), residues: 64
  sheet: -1.04 (0.38), residues: 183
  loop : -0.45 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 269 
 HIS   0.005   0.001   HIS B 274 
 PHE   0.019   0.002   PHE B 311 
 TYR   0.010   0.001   TYR A 465 
 ARG   0.006   0.001   ARG B 409 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03433 (  125)
  hydrogen bonds       : angle       6.67971 (  318)
  SS BOND              : bond        0.00169 (   17)
  SS BOND              : angle       0.64010 (   34)
  covalent geometry    : bond        0.00278 ( 5216)
  covalent geometry    : angle       0.59310 ( 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
  92 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.529 
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: 0.9207 (OUTLIER) cc_final: 0.8865 (pp)
REVERT: A  345 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7504 (mt-10)
REVERT: A  353 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8464 (p0)
REVERT: A  537 LYS cc_start: 0.8313 (tptt) cc_final: 0.7995 (tptp)
REVERT: A  610 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8645 (pt)
REVERT: B  178 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8841 (tt0)
REVERT: B  188 MET cc_start: 0.7765 (mtt) cc_final: 0.7154 (mmt)
REVERT: B  202 ASP cc_start: 0.8455 (p0) cc_final: 0.7538 (t0)
REVERT: B  210 MET cc_start: 0.7750 (tpp) cc_final: 0.7496 (tpp)
REVERT: B  291 ILE cc_start: 0.7558 (mt) cc_final: 0.7341 (mp)
REVERT: B  334 HIS cc_start: 0.8904 (t-90) cc_final: 0.8174 (t-90)
REVERT: B  362 LYS cc_start: 0.9231 (mttm) cc_final: 0.9028 (mttm)
REVERT: B  395 GLU cc_start: 0.9102 (tp30) cc_final: 0.8740 (tp30)
REVERT: B  417 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8481 (m-30)
REVERT: B  488 MET cc_start: 0.6648 (mtp) cc_final: 0.6285 (mtp)
  outliers start: 21
  outliers final: 10
  residues processed: 88
  average time/residue: 0.1688
  time to fit residues: 19.5805
Evaluate side-chains
  78 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
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 A residue  610 LEU
Chi-restraints excluded: chain B residue  157 ILE
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 353 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.098572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.083624 restraints weight = 21812.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.4045 rms_B_bonded: 6.99
r_work (final): 0.4045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.5751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5233  Z= 0.125
  Angle     :  0.596   6.946   7128  Z= 0.308
  Chirality :  0.046   0.228    755
  Planarity :  0.004   0.036    923
  Dihedral  :  4.567  20.512    704
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 17.41
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.08 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 22.09 %
    Favored  : 74.78 %
  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: -1.00 (0.32), residues: 649
  helix: -0.21 (0.72), residues: 58
  sheet: -0.96 (0.38), residues: 178
  loop : -0.53 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 269 
 HIS   0.005   0.001   HIS B 274 
 PHE   0.019   0.002   PHE B 311 
 TYR   0.010   0.001   TYR B 222 
 ARG   0.005   0.001   ARG B 409 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03247 (  125)
  hydrogen bonds       : angle       6.63373 (  318)
  SS BOND              : bond        0.00160 (   17)
  SS BOND              : angle       0.66494 (   34)
  covalent geometry    : bond        0.00279 ( 5216)
  covalent geometry    : angle       0.59534 ( 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
  92 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.996 
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: 0.9244 (OUTLIER) cc_final: 0.8978 (pp)
REVERT: A  345 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7495 (mt-10)
REVERT: A  501 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.6976 (t80)
REVERT: A  537 LYS cc_start: 0.8304 (tptt) cc_final: 0.7990 (tptp)
REVERT: A  610 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8736 (pt)
REVERT: B  178 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8836 (tt0)
REVERT: B  188 MET cc_start: 0.7771 (mtt) cc_final: 0.7161 (mmt)
REVERT: B  202 ASP cc_start: 0.8470 (p0) cc_final: 0.7666 (t0)
REVERT: B  321 PHE cc_start: 0.8759 (m-10) cc_final: 0.8550 (m-10)
REVERT: B  332 ILE cc_start: 0.7842 (mm) cc_final: 0.7561 (mp)
REVERT: B  334 HIS cc_start: 0.8962 (t-90) cc_final: 0.8213 (t-90)
REVERT: B  362 LYS cc_start: 0.9216 (mttm) cc_final: 0.9010 (mttm)
REVERT: B  417 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8500 (m-30)
REVERT: B  488 MET cc_start: 0.6740 (mtp) cc_final: 0.6303 (mtp)
  outliers start: 18
  outliers final: 13
  residues processed: 87
  average time/residue: 0.2290
  time to fit residues: 26.7957
Evaluate side-chains
  82 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
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 A residue  469 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  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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 3 optimal weight:    0.2980
   chunk 12 optimal weight:    0.7980
   chunk 41 optimal weight:    6.9990
   chunk 63 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 26 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 353 ASN
B 198 GLN
** 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 = 0.4363 r_free = 0.4363 target = 0.098113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.083273 restraints weight = 22237.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.4051 rms_B_bonded: 7.03
r_work (final): 0.4051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.5938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   5233  Z= 0.121
  Angle     :  0.630   9.935   7128  Z= 0.327
  Chirality :  0.046   0.205    755
  Planarity :  0.004   0.034    923
  Dihedral  :  4.531  21.673    704
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 15.89
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.93 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 22.26 %
    Favored  : 74.43 %
  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: -0.97 (0.32), residues: 649
  helix: -0.18 (0.72), residues: 58
  sheet: -0.99 (0.38), residues: 179
  loop : -0.48 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP B 269 
 HIS   0.005   0.001   HIS B 274 
 PHE   0.024   0.002   PHE B 311 
 TYR   0.010   0.001   TYR B 222 
 ARG   0.004   0.001   ARG B 409 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03097 (  125)
  hydrogen bonds       : angle       6.49676 (  318)
  SS BOND              : bond        0.00144 (   17)
  SS BOND              : angle       0.63973 (   34)
  covalent geometry    : bond        0.00272 ( 5216)
  covalent geometry    : angle       0.63002 ( 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
  91 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.539 
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: 0.9221 (OUTLIER) cc_final: 0.8819 (pp)
REVERT: A  345 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7464 (mt-10)
REVERT: A  501 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.7008 (t80)
REVERT: A  537 LYS cc_start: 0.8251 (tptt) cc_final: 0.7924 (tptp)
REVERT: A  610 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8771 (pt)
REVERT: B  188 MET cc_start: 0.7711 (mtt) cc_final: 0.7104 (mmt)
REVERT: B  202 ASP cc_start: 0.8473 (p0) cc_final: 0.7665 (t0)
REVERT: B  210 MET cc_start: 0.7956 (tpp) cc_final: 0.7513 (tpp)
REVERT: B  320 MET cc_start: 0.8933 (pmm) cc_final: 0.8516 (pmm)
REVERT: B  332 ILE cc_start: 0.7848 (mm) cc_final: 0.7559 (mp)
REVERT: B  334 HIS cc_start: 0.8985 (t-90) cc_final: 0.8248 (t-90)
REVERT: B  378 LEU cc_start: 0.8180 (tp) cc_final: 0.7622 (tp)
REVERT: B  417 ASP cc_start: 0.9014 (OUTLIER) cc_final: 0.8567 (m-30)
REVERT: B  488 MET cc_start: 0.6772 (mtp) cc_final: 0.6332 (mtp)
  outliers start: 19
  outliers final: 12
  residues processed: 87
  average time/residue: 0.1628
  time to fit residues: 18.9445
Evaluate side-chains
  85 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
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 A residue  469 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  397 LEU
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 28 optimal weight:    0.3980
   chunk 32 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 353 ASN
B 159 GLN
** 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 = 0.4327 r_free = 0.4327 target = 0.096272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.081410 restraints weight = 22466.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.4020 rms_B_bonded: 7.03
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.6327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5233  Z= 0.147
  Angle     :  0.636   7.543   7128  Z= 0.334
  Chirality :  0.046   0.191    755
  Planarity :  0.004   0.033    923
  Dihedral  :  4.625  19.704    704
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 18.62
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.93 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 22.26 %
    Favored  : 73.91 %
  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: -1.01 (0.33), residues: 649
  helix: -0.17 (0.74), residues: 58
  sheet: -0.98 (0.38), residues: 178
  loop : -0.54 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 269 
 HIS   0.004   0.001   HIS B 169 
 PHE   0.033   0.002   PHE A 373 
 TYR   0.010   0.002   TYR B 222 
 ARG   0.006   0.001   ARG B 409 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03381 (  125)
  hydrogen bonds       : angle       6.32138 (  318)
  SS BOND              : bond        0.00248 (   17)
  SS BOND              : angle       0.71344 (   34)
  covalent geometry    : bond        0.00329 ( 5216)
  covalent geometry    : angle       0.63551 ( 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
  92 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 70
  time to evaluate  : 1.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8880 (pp)
REVERT: A  345 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7462 (mt-10)
REVERT: A  501 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.7231 (t80)
REVERT: A  610 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8750 (pt)
REVERT: B  188 MET cc_start: 0.7711 (mtt) cc_final: 0.7129 (mmt)
REVERT: B  202 ASP cc_start: 0.8541 (p0) cc_final: 0.7736 (t0)
REVERT: B  210 MET cc_start: 0.7977 (tpp) cc_final: 0.7472 (tpp)
REVERT: B  320 MET cc_start: 0.8923 (pmm) cc_final: 0.8211 (pmm)
REVERT: B  334 HIS cc_start: 0.9074 (t-90) cc_final: 0.8237 (t-90)
REVERT: B  362 LYS cc_start: 0.9071 (mttm) cc_final: 0.8613 (mtmm)
REVERT: B  371 MET cc_start: 0.7090 (ptp) cc_final: 0.6821 (ptp)
REVERT: B  404 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8345 (mm)
REVERT: B  417 ASP cc_start: 0.9061 (OUTLIER) cc_final: 0.8598 (m-30)
REVERT: B  488 MET cc_start: 0.6881 (mtp) cc_final: 0.6651 (mtp)
  outliers start: 22
  outliers final: 13
  residues processed: 88
  average time/residue: 0.1948
  time to fit residues: 22.3913
Evaluate side-chains
  84 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
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 A residue  469 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  198 GLN
Chi-restraints excluded: chain B residue  213 ASN
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  404 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:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 353 ASN
** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 193 ASN
** B 277 ASN ** 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 = 0.095240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.080368 restraints weight = 22452.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.4000 rms_B_bonded: 6.93
r_work (final): 0.4000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.6624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   5233  Z= 0.165
  Angle     :  0.689  10.750   7128  Z= 0.356
  Chirality :  0.048   0.217    755
  Planarity :  0.004   0.032    923
  Dihedral  :  4.876  21.957    704
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 20.04
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.24 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 23.13 %
    Favored  : 73.04 %
  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: -0.98 (0.33), residues: 649
  helix:  0.17 (0.78), residues: 53
  sheet: -1.17 (0.38), residues: 177
  loop : -0.45 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B 269 
 HIS   0.005   0.001   HIS B 169 
 PHE   0.026   0.002   PHE A 373 
 TYR   0.021   0.002   TYR B 414 
 ARG   0.006   0.001   ARG B 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03509 (  125)
  hydrogen bonds       : angle       6.29200 (  318)
  SS BOND              : bond        0.00210 (   17)
  SS BOND              : angle       0.76568 (   34)
  covalent geometry    : bond        0.00368 ( 5216)
  covalent geometry    : angle       0.68856 ( 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
  92 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 70
  time to evaluate  : 0.682 
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: 0.9314 (OUTLIER) cc_final: 0.8924 (pp)
REVERT: A  345 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7465 (mt-10)
REVERT: A  501 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.7385 (t80)
REVERT: B  202 ASP cc_start: 0.8512 (p0) cc_final: 0.7693 (t0)
REVERT: B  210 MET cc_start: 0.7978 (tpp) cc_final: 0.7494 (tpp)
REVERT: B  289 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8034 (mm-30)
REVERT: B  320 MET cc_start: 0.8979 (pmm) cc_final: 0.8552 (pmm)
REVERT: B  334 HIS cc_start: 0.9093 (t-90) cc_final: 0.8473 (t-90)
REVERT: B  362 LYS cc_start: 0.9076 (mttm) cc_final: 0.8627 (mtmm)
REVERT: B  371 MET cc_start: 0.7111 (ptp) cc_final: 0.6856 (ptp)
REVERT: B  417 ASP cc_start: 0.9007 (OUTLIER) cc_final: 0.8575 (m-30)
  outliers start: 22
  outliers final: 17
  residues processed: 87
  average time/residue: 0.2195
  time to fit residues: 24.5403
Evaluate side-chains
  86 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
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  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  597 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  198 GLN
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  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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 52 optimal weight:    0.0060
   chunk 21 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 41 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 40 optimal weight:    7.9990
   chunk 51 optimal weight:    6.9990
   chunk 37 optimal weight:    7.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.7800

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

Flipped N/Q/H residues before XYZ refinement:
A 353 ASN
** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.096773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.081791 restraints weight = 22210.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.4028 rms_B_bonded: 6.95
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.6723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   5233  Z= 0.138
  Angle     :  0.694  11.956   7128  Z= 0.357
  Chirality :  0.047   0.169    755
  Planarity :  0.004   0.033    923
  Dihedral  :  4.839  25.897    704
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 18.52
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.93 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 24.00 %
    Favored  : 72.70 %
  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: -0.98 (0.33), residues: 649
  helix:  0.19 (0.78), residues: 53
  sheet: -1.15 (0.40), residues: 165
  loop : -0.49 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 269 
 HIS   0.005   0.001   HIS B 169 
 PHE   0.024   0.002   PHE A 373 
 TYR   0.024   0.002   TYR B 414 
 ARG   0.005   0.001   ARG B 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03145 (  125)
  hydrogen bonds       : angle       6.20105 (  318)
  SS BOND              : bond        0.00192 (   17)
  SS BOND              : angle       0.68889 (   34)
  covalent geometry    : bond        0.00317 ( 5216)
  covalent geometry    : angle       0.69419 ( 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
  87 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8911 (pp)
REVERT: A  345 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7447 (mt-10)
REVERT: A  501 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.7324 (t80)
REVERT: A  610 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8733 (pt)
REVERT: B  188 MET cc_start: 0.7655 (mtt) cc_final: 0.6550 (mtp)
REVERT: B  202 ASP cc_start: 0.8510 (p0) cc_final: 0.7684 (t0)
REVERT: B  289 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8015 (mm-30)
REVERT: B  320 MET cc_start: 0.9028 (pmm) cc_final: 0.8660 (pmm)
REVERT: B  332 ILE cc_start: 0.7848 (mm) cc_final: 0.7569 (mp)
REVERT: B  334 HIS cc_start: 0.9060 (t-90) cc_final: 0.8259 (t-90)
REVERT: B  362 LYS cc_start: 0.9043 (mttm) cc_final: 0.8581 (mtmm)
REVERT: B  371 MET cc_start: 0.7095 (ptp) cc_final: 0.6826 (ptp)
REVERT: B  417 ASP cc_start: 0.8898 (OUTLIER) cc_final: 0.8449 (m-30)
  outliers start: 19
  outliers final: 15
  residues processed: 83
  average time/residue: 0.1596
  time to fit residues: 17.6531
Evaluate side-chains
  85 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
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 A residue  469 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  213 ASN
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  404 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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 56 optimal weight:    0.6980
   chunk 53 optimal weight:   10.0000
   chunk 60 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 277 ASN ** 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 = 0.4294 r_free = 0.4294 target = 0.094548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.079808 restraints weight = 22651.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3991 rms_B_bonded: 6.91
r_work (final): 0.3991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.7000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   5233  Z= 0.173
  Angle     :  0.718  11.602   7128  Z= 0.368
  Chirality :  0.047   0.163    755
  Planarity :  0.004   0.034    923
  Dihedral  :  4.950  25.148    704
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 21.66
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.63 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 23.83 %
    Favored  : 72.35 %
  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: -1.11 (0.33), residues: 649
  helix: -0.11 (0.74), residues: 59
  sheet: -1.23 (0.38), residues: 177
  loop : -0.54 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 269 
 HIS   0.005   0.001   HIS B 169 
 PHE   0.021   0.002   PHE A 373 
 TYR   0.021   0.002   TYR B 414 
 ARG   0.005   0.001   ARG B 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03492 (  125)
  hydrogen bonds       : angle       6.32309 (  318)
  SS BOND              : bond        0.00213 (   17)
  SS BOND              : angle       0.72611 (   34)
  covalent geometry    : bond        0.00393 ( 5216)
  covalent geometry    : angle       0.71840 ( 7094)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3665.06 seconds
wall clock time: 67 minutes 15.07 seconds (4035.07 seconds total)