Starting phenix.real_space_refine
on Thu Mar  6 05:45:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yoy_39460/03_2025/8yoy_39460.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yoy_39460/03_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_39460/03_2025/8yoy_39460.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yoy_39460/03_2025/8yoy_39460.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yoy_39460/03_2025/8yoy_39460.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yoy_39460/03_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-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5081
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2248
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2248
          Classifications: {'peptide': 289}
          Link IDs: {'PTRANS': 14, 'TRANS': 274}
    Chain: "B"
      Number of atoms: 2833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 364, 2833
          Classifications: {'peptide': 364}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 346}
  Time building chain proxies: 3.79, per 1000 atoms: 0.75
  Number of scatterers: 5081
  At special positions: 0
  Unit cell: (63.99, 78.57, 136.89, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      47     16.00
     O     970      8.00
     N     879      7.00
     C    3185      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.19
  Conformation dependent library (CDL) restraints added in 634.1 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: 0.65
  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: 1.45 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:             1.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     16.710
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.370
-------------------------------------------------------------------------------
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   5216  Z= 0.227
  Angle     :  0.500   5.588   7094  Z= 0.270
  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 

*********************** 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  : 0.589 
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: 0.2410
  time to fit residues: 44.7729
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  : 0.556 
-------------------------------------------------------------------------------
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   5216  Z= 0.279
  Angle     :  0.674   8.795   7094  Z= 0.363
  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 

*********************** 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  : 0.743 
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: 0.2901
  time to fit residues: 35.8337
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  : 0.692 
-------------------------------------------------------------------------------
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:    2.9990
   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:    1.4784

-------------------------------------------------------------------------------
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 ** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.098900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.084098 restraints weight = 21732.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.4052 rms_B_bonded: 6.96
r_work (final): 0.4052
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4051
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4051 r_free = 0.4051    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4049 r_free = 0.4049    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4049
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.4810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5216  Z= 0.255
  Angle     :  0.648  10.747   7094  Z= 0.340
  Chirality :  0.048   0.235    755
  Planarity :  0.005   0.048    923
  Dihedral  :  4.835  21.846    704
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 19.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 18.96 %
    Favored  : 76.70 %
  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: -1.34 (0.32), residues: 649
  helix: -1.71 (0.54), residues: 76
  sheet: -0.98 (0.40), residues: 175
  loop : -0.60 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 380 
 HIS   0.004   0.001   HIS A 512 
 PHE   0.030   0.002   PHE A 373 
 TYR   0.015   0.002   TYR A 465 
 ARG   0.014   0.001   ARG B 409 

*********************** 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  : 0.978 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8964 (pp)
REVERT: A  345 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7600 (mt-10)
REVERT: A  604 THR cc_start: 0.6118 (OUTLIER) cc_final: 0.5886 (t)
REVERT: B  178 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8877 (tt0)
REVERT: B  188 MET cc_start: 0.7808 (mtt) cc_final: 0.7302 (mmt)
REVERT: B  200 ILE cc_start: 0.8909 (pt) cc_final: 0.8418 (mm)
REVERT: B  202 ASP cc_start: 0.8433 (p0) cc_final: 0.7489 (t0)
REVERT: B  317 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8376 (tp-100)
REVERT: B  320 MET cc_start: 0.8062 (ptp) cc_final: 0.7572 (ptp)
REVERT: B  401 LYS cc_start: 0.8882 (mttt) cc_final: 0.8656 (pttp)
REVERT: B  417 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.8404 (m-30)
  outliers start: 25
  outliers final: 11
  residues processed: 78
  average time/residue: 0.1967
  time to fit residues: 20.2440
Evaluate side-chains
  74 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 54 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 42 optimal weight:    0.0770
   chunk 29 optimal weight:    0.0270
   overall best weight:    0.4998

-------------------------------------------------------------------------------
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 = 0.4390 r_free = 0.4390 target = 0.100464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.084897 restraints weight = 22035.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.4088 rms_B_bonded: 7.23
r_work (final): 0.4088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7331
moved from start:          0.4990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5216  Z= 0.174
  Angle     :  0.589   7.322   7094  Z= 0.309
  Chirality :  0.046   0.156    755
  Planarity :  0.004   0.039    923
  Dihedral  :  4.554  19.211    704
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 16.50
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.24 %
    Favored  : 94.61 %
  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: -1.25 (0.32), residues: 649
  helix: -1.13 (0.59), residues: 71
  sheet: -0.87 (0.40), residues: 172
  loop : -0.70 (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   0.017   0.002   PHE A 481 
 TYR   0.012   0.001   TYR A 465 
 ARG   0.006   0.001   ARG B 409 

*********************** 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  : 0.899 
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  345 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7555 (mt-10)
REVERT: A  537 LYS cc_start: 0.8338 (tptt) cc_final: 0.8017 (tptp)
REVERT: A  604 THR cc_start: 0.6261 (OUTLIER) cc_final: 0.6032 (t)
REVERT: B  188 MET cc_start: 0.7785 (mtt) cc_final: 0.7162 (mmt)
REVERT: B  202 ASP cc_start: 0.8379 (p0) cc_final: 0.8140 (p0)
REVERT: B  210 MET cc_start: 0.7556 (tpp) cc_final: 0.7300 (tpp)
REVERT: B  320 MET cc_start: 0.8079 (ptp) cc_final: 0.6792 (ptp)
REVERT: B  332 ILE cc_start: 0.7825 (mm) cc_final: 0.7532 (mp)
REVERT: B  334 HIS cc_start: 0.8759 (t-90) cc_final: 0.8131 (t-90)
REVERT: B  359 ASP cc_start: 0.9634 (m-30) cc_final: 0.9145 (p0)
REVERT: B  362 LYS cc_start: 0.9139 (mttp) cc_final: 0.8819 (mptt)
REVERT: B  395 GLU cc_start: 0.9207 (tp30) cc_final: 0.8956 (tp30)
REVERT: B  417 ASP cc_start: 0.8867 (OUTLIER) cc_final: 0.8401 (m-30)
REVERT: B  488 MET cc_start: 0.6616 (mtp) cc_final: 0.6283 (mtp)
  outliers start: 19
  outliers final: 9
  residues processed: 84
  average time/residue: 0.2004
  time to fit residues: 22.5142
Evaluate side-chains
  72 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  460 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:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 50 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 26 optimal weight:    0.7980
   chunk 46 optimal weight:    7.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    1.2382

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 433 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.096689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.081781 restraints weight = 21866.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.4015 rms_B_bonded: 6.86
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.5733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5216  Z= 0.216
  Angle     :  0.610   6.859   7094  Z= 0.321
  Chirality :  0.046   0.165    755
  Planarity :  0.004   0.040    923
  Dihedral  :  4.756  20.435    704
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 18.12
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.70 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 22.78 %
    Favored  : 74.26 %
  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: -1.13 (0.32), residues: 649
  helix: -0.36 (0.71), residues: 58
  sheet: -1.11 (0.38), residues: 179
  loop : -0.58 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 380 
 HIS   0.004   0.001   HIS B 274 
 PHE   0.016   0.002   PHE B 311 
 TYR   0.010   0.002   TYR A 465 
 ARG   0.006   0.001   ARG B 409 

*********************** 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
  87 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7535 (mt-10)
REVERT: A  610 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8681 (pt)
REVERT: B  178 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8832 (tt0)
REVERT: B  188 MET cc_start: 0.7726 (mtt) cc_final: 0.7204 (mmt)
REVERT: B  202 ASP cc_start: 0.8574 (p0) cc_final: 0.7653 (t0)
REVERT: B  334 HIS cc_start: 0.8989 (t-90) cc_final: 0.8194 (t-90)
REVERT: B  362 LYS cc_start: 0.9188 (mttp) cc_final: 0.8755 (mtmm)
REVERT: B  395 GLU cc_start: 0.9090 (tp30) cc_final: 0.8689 (tp30)
REVERT: B  417 ASP cc_start: 0.9062 (OUTLIER) cc_final: 0.8586 (m-30)
  outliers start: 17
  outliers final: 12
  residues processed: 84
  average time/residue: 0.2025
  time to fit residues: 23.2298
Evaluate side-chains
  75 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  469 VAL
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 44 optimal weight:    0.0670
   chunk 47 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 58 optimal weight:    8.9990
   chunk 8 optimal weight:    0.6980
   chunk 37 optimal weight:    0.2980
   overall best weight:    0.5318

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.098270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.082888 restraints weight = 21465.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.4054 rms_B_bonded: 7.17
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.5893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5216  Z= 0.173
  Angle     :  0.610   7.344   7094  Z= 0.314
  Chirality :  0.047   0.219    755
  Planarity :  0.004   0.036    923
  Dihedral  :  4.571  20.540    704
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 15.69
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.16 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 22.78 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.32), residues: 649
  helix: -0.25 (0.70), residues: 58
  sheet: -1.00 (0.40), residues: 166
  loop : -0.55 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 269 
 HIS   0.005   0.001   HIS B 274 
 PHE   0.020   0.002   PHE B 311 
 TYR   0.010   0.001   TYR B 222 
 ARG   0.004   0.001   ARG B 409 

*********************** 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
  84 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.554 
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  345 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7437 (mt-10)
REVERT: A  501 TYR cc_start: 0.7783 (OUTLIER) cc_final: 0.7110 (t80)
REVERT: A  537 LYS cc_start: 0.8317 (tptt) cc_final: 0.8001 (tptp)
REVERT: A  610 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8729 (pt)
REVERT: B  188 MET cc_start: 0.7733 (mtt) cc_final: 0.7180 (mmt)
REVERT: B  202 ASP cc_start: 0.8521 (p0) cc_final: 0.7671 (t0)
REVERT: B  210 MET cc_start: 0.7482 (tpp) cc_final: 0.7247 (tpp)
REVERT: B  269 TRP cc_start: 0.8389 (p90) cc_final: 0.8056 (p90)
REVERT: B  332 ILE cc_start: 0.7811 (mm) cc_final: 0.7521 (mp)
REVERT: B  334 HIS cc_start: 0.8974 (t-90) cc_final: 0.8258 (t-90)
REVERT: B  362 LYS cc_start: 0.9115 (mttp) cc_final: 0.8693 (mtmm)
REVERT: B  417 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8518 (m-30)
  outliers start: 15
  outliers final: 10
  residues processed: 81
  average time/residue: 0.1852
  time to fit residues: 19.9870
Evaluate side-chains
  75 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  405 ILE
Chi-restraints excluded: chain B residue  407 THR
Chi-restraints excluded: chain B residue  410 CYS
Chi-restraints excluded: chain B residue  415 VAL
Chi-restraints excluded: chain B residue  417 ASP
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  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:    9.9990
   chunk 3 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   chunk 41 optimal weight:    7.9990
   chunk 63 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 43 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    1.9786

-------------------------------------------------------------------------------
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 193 ASN
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.092213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.077368 restraints weight = 22378.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 6.87
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.6685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   5216  Z= 0.300
  Angle     :  0.694   8.351   7094  Z= 0.369
  Chirality :  0.048   0.200    755
  Planarity :  0.004   0.038    923
  Dihedral  :  4.968  19.737    704
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 23.38
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.39 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 23.30 %
    Favored  : 73.22 %
  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: -1.31 (0.32), residues: 649
  helix: -0.64 (0.68), residues: 64
  sheet: -1.27 (0.38), residues: 177
  loop : -0.65 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 380 
 HIS   0.004   0.002   HIS B 169 
 PHE   0.027   0.003   PHE A 373 
 TYR   0.017   0.002   TYR A 465 
 ARG   0.009   0.001   ARG A 464 

*********************** 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
  89 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  501 TYR cc_start: 0.7697 (OUTLIER) cc_final: 0.7435 (t80)
REVERT: B  178 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8804 (tt0)
REVERT: B  188 MET cc_start: 0.7692 (mtt) cc_final: 0.6693 (mtp)
REVERT: B  202 ASP cc_start: 0.8665 (p0) cc_final: 0.7708 (t0)
REVERT: B  320 MET cc_start: 0.9020 (pmm) cc_final: 0.8615 (pmm)
REVERT: B  334 HIS cc_start: 0.9254 (t-90) cc_final: 0.8672 (t-90)
REVERT: B  362 LYS cc_start: 0.9132 (mttp) cc_final: 0.8673 (mtmm)
REVERT: B  366 LEU cc_start: 0.7518 (tp) cc_final: 0.7314 (tp)
REVERT: B  371 MET cc_start: 0.7354 (ptp) cc_final: 0.7041 (ptp)
REVERT: B  417 ASP cc_start: 0.9118 (OUTLIER) cc_final: 0.8585 (m-30)
  outliers start: 20
  outliers final: 14
  residues processed: 85
  average time/residue: 0.1908
  time to fit residues: 20.8024
Evaluate side-chains
  75 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 59
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  446 ARG
Chi-restraints excluded: chain A residue  458 HIS
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  488 HIS
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  213 ASN
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  410 CYS
Chi-restraints excluded: chain B residue  415 VAL
Chi-restraints excluded: chain B residue  417 ASP
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  478 MET
Chi-restraints excluded: chain B residue  479 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 56 optimal weight:    7.9990
   chunk 43 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 198 GLN
** 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 = 0.4293 r_free = 0.4293 target = 0.094227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.079324 restraints weight = 22143.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3985 rms_B_bonded: 6.85
r_work (final): 0.3985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.6788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5216  Z= 0.237
  Angle     :  0.672   7.565   7094  Z= 0.347
  Chirality :  0.048   0.210    755
  Planarity :  0.004   0.035    923
  Dihedral  :  4.865  21.575    704
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 20.04
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.08 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 23.65 %
    Favored  : 73.22 %
  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: -1.23 (0.32), residues: 649
  helix: -0.36 (0.72), residues: 58
  sheet: -1.14 (0.38), residues: 175
  loop : -0.68 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 269 
 HIS   0.005   0.001   HIS B 169 
 PHE   0.021   0.002   PHE A 373 
 TYR   0.018   0.002   TYR B 414 
 ARG   0.013   0.001   ARG B 316 

*********************** 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
  86 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
REVERT: A  345 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7458 (mt-10)
REVERT: A  446 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8323 (ptt-90)
REVERT: A  501 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.7387 (t80)
REVERT: A  537 LYS cc_start: 0.8324 (tptt) cc_final: 0.8109 (tptp)
REVERT: A  610 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8750 (pt)
REVERT: B  178 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8754 (tp30)
REVERT: B  188 MET cc_start: 0.7669 (mtt) cc_final: 0.6563 (mtp)
REVERT: B  202 ASP cc_start: 0.8369 (p0) cc_final: 0.7594 (t0)
REVERT: B  210 MET cc_start: 0.7556 (tpp) cc_final: 0.7246 (tpp)
REVERT: B  320 MET cc_start: 0.9123 (pmm) cc_final: 0.8570 (pmm)
REVERT: B  334 HIS cc_start: 0.9148 (t-90) cc_final: 0.8547 (t-90)
REVERT: B  362 LYS cc_start: 0.9110 (mttp) cc_final: 0.8720 (mtmm)
REVERT: B  371 MET cc_start: 0.7363 (ptp) cc_final: 0.7101 (ptp)
REVERT: B  417 ASP cc_start: 0.8999 (OUTLIER) cc_final: 0.8503 (m-30)
  outliers start: 18
  outliers final: 10
  residues processed: 84
  average time/residue: 0.1821
  time to fit residues: 20.1710
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  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  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:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 26 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 24 optimal weight:    9.9990
   chunk 3 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 159 GLN
** 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 = 0.4299 r_free = 0.4299 target = 0.094913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.079843 restraints weight = 21852.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3994 rms_B_bonded: 6.93
r_work (final): 0.3994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.6966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   5216  Z= 0.240
  Angle     :  0.689   8.197   7094  Z= 0.355
  Chirality :  0.048   0.195    755
  Planarity :  0.004   0.036    923
  Dihedral  :  4.856  24.426    704
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 20.75
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.39 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 24.00 %
    Favored  : 72.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.33), residues: 649
  helix: -0.28 (0.72), residues: 58
  sheet: -1.15 (0.40), residues: 167
  loop : -0.71 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 269 
 HIS   0.005   0.001   HIS B 169 
 PHE   0.018   0.002   PHE A 373 
 TYR   0.019   0.002   TYR B 414 
 ARG   0.009   0.001   ARG B 316 

*********************** 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
  85 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 67
  time to evaluate  : 1.263 
Fit side-chains
   revert: symmetry clash
REVERT: A  464 ARG cc_start: 0.8717 (mpt-90) cc_final: 0.8258 (mtt90)
REVERT: A  501 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.7415 (t80)
REVERT: A  537 LYS cc_start: 0.8262 (tptt) cc_final: 0.8050 (tptp)
REVERT: A  610 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8706 (pt)
REVERT: B  178 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8735 (tp30)
REVERT: B  188 MET cc_start: 0.7706 (mtt) cc_final: 0.6550 (mtp)
REVERT: B  202 ASP cc_start: 0.8317 (p0) cc_final: 0.7549 (t0)
REVERT: B  210 MET cc_start: 0.7609 (tpp) cc_final: 0.7385 (tpp)
REVERT: B  289 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8120 (mm-30)
REVERT: B  320 MET cc_start: 0.9117 (pmm) cc_final: 0.8512 (pmm)
REVERT: B  334 HIS cc_start: 0.9150 (t-90) cc_final: 0.8357 (t-90)
REVERT: B  362 LYS cc_start: 0.9073 (mttp) cc_final: 0.8673 (mtmm)
REVERT: B  371 MET cc_start: 0.7418 (ptp) cc_final: 0.7160 (ptp)
REVERT: B  417 ASP cc_start: 0.9022 (OUTLIER) cc_final: 0.8522 (m-30)
  outliers start: 18
  outliers final: 13
  residues processed: 82
  average time/residue: 0.2631
  time to fit residues: 30.9969
Evaluate side-chains
  79 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 63
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  405 ILE
Chi-restraints excluded: chain B residue  410 CYS
Chi-restraints excluded: chain B residue  415 VAL
Chi-restraints excluded: chain B residue  417 ASP
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  478 MET
Chi-restraints excluded: chain B residue  479 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 41 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 40 optimal weight:    8.9990
   chunk 51 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
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 317 GLN
** 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 = 0.4239 r_free = 0.4239 target = 0.091228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.076365 restraints weight = 22155.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3934 rms_B_bonded: 6.82
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.7404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   5216  Z= 0.312
  Angle     :  0.743   8.971   7094  Z= 0.387
  Chirality :  0.049   0.178    755
  Planarity :  0.004   0.038    923
  Dihedral  :  5.126  24.580    704
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 25.20
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.78 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 24.17 %
    Favored  : 72.52 %
  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: -1.42 (0.32), residues: 649
  helix: -0.43 (0.73), residues: 58
  sheet: -1.45 (0.38), residues: 172
  loop : -0.74 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 269 
 HIS   0.007   0.002   HIS B 169 
 PHE   0.018   0.002   PHE B 311 
 TYR   0.017   0.002   TYR B 414 
 ARG   0.008   0.001   ARG B 316 

********************** 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
  80 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
REVERT: A  446 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8300 (ptt-90)
REVERT: A  501 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.7318 (t80)
REVERT: A  537 LYS cc_start: 0.8306 (tptt) cc_final: 0.8087 (tptp)
REVERT: B  178 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8911 (pm20)
REVERT: B  188 MET cc_start: 0.7596 (mtt) cc_final: 0.6471 (mtp)
REVERT: B  202 ASP cc_start: 0.8313 (p0) cc_final: 0.7530 (t0)
REVERT: B  210 MET cc_start: 0.7635 (tpp) cc_final: 0.7418 (tpp)
REVERT: B  239 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7925 (pp)
REVERT: B  269 TRP cc_start: 0.8441 (p90) cc_final: 0.7915 (p90)
REVERT: B  289 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8217 (mm-30)
REVERT: B  334 HIS cc_start: 0.9232 (t-90) cc_final: 0.8762 (t-90)
REVERT: B  362 LYS cc_start: 0.9097 (mttp) cc_final: 0.8863 (mptt)
REVERT: B  371 MET cc_start: 0.7612 (ptp) cc_final: 0.7327 (ptp)
REVERT: B  417 ASP cc_start: 0.9064 (OUTLIER) cc_final: 0.8576 (m-30)
  outliers start: 19
  outliers final: 14
  residues processed: 77
  average time/residue: 0.1770
  time to fit residues: 18.8830
Evaluate side-chains
  74 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 ASP
Chi-restraints excluded: chain A residue  446 ARG
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  213 ASN
Chi-restraints excluded: chain B residue  239 LEU
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  405 ILE
Chi-restraints excluded: chain B residue  410 CYS
Chi-restraints excluded: chain B residue  415 VAL
Chi-restraints excluded: chain B residue  417 ASP
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  478 MET
Chi-restraints excluded: chain B residue  479 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 53 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 46 optimal weight:    0.0770
   chunk 33 optimal weight:    4.9990
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.7138

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

Flipped N/Q/H residues before XYZ refinement:
** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4296 r_free = 0.4296 target = 0.095088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.080423 restraints weight = 22189.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.3994 rms_B_bonded: 6.87
r_work (final): 0.3994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.7337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5216  Z= 0.212
  Angle     :  0.694   9.924   7094  Z= 0.359
  Chirality :  0.048   0.155    755
  Planarity :  0.004   0.036    923
  Dihedral  :  4.899  23.102    704
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 19.94
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.70 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 24.87 %
    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: -1.24 (0.33), residues: 649
  helix: -0.22 (0.74), residues: 58
  sheet: -1.35 (0.37), residues: 172
  loop : -0.62 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 269 
 HIS   0.005   0.001   HIS B 169 
 PHE   0.019   0.002   PHE B 311 
 TYR   0.013   0.001   TYR B 414 
 ARG   0.008   0.001   ARG B 316 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3474.20 seconds
wall clock time: 63 minutes 57.48 seconds (3837.48 seconds total)