Starting phenix.real_space_refine
on Fri Aug 22 15:35:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yoy_39460/08_2025/8yoy_39460.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yoy_39460/08_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_39460/08_2025/8yoy_39460.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yoy_39460/08_2025/8yoy_39460.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yoy_39460/08_2025/8yoy_39460.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yoy_39460/08_2025/8yoy_39460.cif"
  }
  resolution = 3.21
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.018
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.59, per 1000 atoms: 0.31
  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: 0.42
  Conformation dependent library (CDL) restraints added in 172.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.19
  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: 0.73

  Time building geometry restraints manager: 0.60 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:             1.880
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     6.760
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.110
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.003   0.000   ARG B 409 
 TYR   0.008   0.001   TYR B 222 
 PHE   0.005   0.001   PHE A 391 
 TRP   0.010   0.001   TRP A 515 
 HIS   0.003   0.000   HIS B 296 

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

*********************** 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  : 0.229 
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: 0.0844
  time to fit residues: 15.9116
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  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    0.2980
   chunk 33 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0970
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.1980
   chunk 27 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   overall best weight:    1.3182

-------------------------------------------------------------------------------
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 = 0.4439 r_free = 0.4439 target = 0.103892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.088413 restraints weight = 20498.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.4148 rms_B_bonded: 7.14
r_work (final): 0.4148
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4149
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4149 r_free = 0.4149    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4150 r_free = 0.4150    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4150
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.3747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5233  Z= 0.175
  Angle     :  0.672   9.383   7128  Z= 0.360
  Chirality :  0.048   0.171    755
  Planarity :  0.005   0.051    923
  Dihedral  :  4.703  19.050    704
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 15.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 18.96 %
    Favored  : 78.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.32 (0.32), residues: 649
  helix: -1.89 (0.52), residues: 77
  sheet: -0.81 (0.40), residues: 175
  loop : -0.62 (0.31), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 409 
 TYR   0.009   0.001   TYR B 474 
 PHE   0.024   0.002   PHE B 311 
 TRP   0.030   0.002   TRP B 168 
 HIS   0.009   0.002   HIS B 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 5216)
  covalent geometry    : angle       0.67020 ( 7094)
  SS BOND              : bond        0.00361 (   17)
  SS BOND              : angle       0.92802 (   34)
  hydrogen bonds       : bond        0.04404 (  125)
  hydrogen bonds       : angle       7.88070 (  318)

*********************** 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
  98 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.220 
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: 0.7914 (mt-10) cc_final: 0.7622 (mt-10)
REVERT: A  353 ASN cc_start: 0.8848 (t0) cc_final: 0.8327 (m110)
REVERT: A  437 ASN cc_start: 0.9302 (OUTLIER) cc_final: 0.9085 (p0)
REVERT: A  589 ASN cc_start: 0.7963 (t0) cc_final: 0.7515 (p0)
REVERT: A  604 THR cc_start: 0.5653 (OUTLIER) cc_final: 0.5378 (t)
REVERT: B  178 GLU cc_start: 0.9280 (tt0) cc_final: 0.8924 (tt0)
REVERT: B  188 MET cc_start: 0.7874 (mtt) cc_final: 0.7013 (mtp)
REVERT: B  202 ASP cc_start: 0.8297 (p0) cc_final: 0.8033 (p0)
REVERT: B  239 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7626 (tp)
REVERT: B  317 GLN cc_start: 0.8424 (mm-40) cc_final: 0.8057 (mm-40)
REVERT: B  417 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8191 (m-30)
REVERT: B  454 TRP cc_start: 0.7610 (m100) cc_final: 0.6940 (m100)
REVERT: B  488 MET cc_start: 0.6762 (mtp) cc_final: 0.6493 (mtp)
  outliers start: 16
  outliers final: 3
  residues processed: 93
  average time/residue: 0.0758
  time to fit residues: 8.9757
Evaluate side-chains
  65 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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 6 optimal weight:    4.9990
   chunk 56 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 24 optimal weight:    9.9990
   chunk 21 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
B 198 GLN
B 253 GLN
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 = 0.4367 r_free = 0.4367 target = 0.099614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.084524 restraints weight = 21926.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.4070 rms_B_bonded: 7.08
r_work (final): 0.4070
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4082
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4082 r_free = 0.4082    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4081 r_free = 0.4081    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4081
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.4617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5233  Z= 0.157
  Angle     :  0.631  10.026   7128  Z= 0.331
  Chirality :  0.048   0.208    755
  Planarity :  0.005   0.047    923
  Dihedral  :  4.752  21.506    704
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 17.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 19.30 %
    Favored  : 76.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.33 (0.32), residues: 649
  helix: -1.63 (0.55), residues: 77
  sheet: -0.89 (0.40), residues: 173
  loop : -0.65 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 409 
 TYR   0.014   0.002   TYR A 465 
 PHE   0.031   0.002   PHE A 373 
 TRP   0.032   0.002   TRP B 380 
 HIS   0.004   0.001   HIS B 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 5216)
  covalent geometry    : angle       0.63072 ( 7094)
  SS BOND              : bond        0.00211 (   17)
  SS BOND              : angle       0.69841 (   34)
  hydrogen bonds       : bond        0.04293 (  125)
  hydrogen bonds       : angle       6.95997 (  318)

*********************** 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
  85 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 63
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7616 (mt-10)
REVERT: A  353 ASN cc_start: 0.8864 (t0) cc_final: 0.8454 (m110)
REVERT: A  604 THR cc_start: 0.5994 (OUTLIER) cc_final: 0.5748 (t)
REVERT: B  178 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8842 (tt0)
REVERT: B  188 MET cc_start: 0.7827 (mtt) cc_final: 0.7253 (mmt)
REVERT: B  202 ASP cc_start: 0.8444 (p0) cc_final: 0.8208 (p0)
REVERT: B  317 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8355 (tp-100)
REVERT: B  320 MET cc_start: 0.8032 (ptp) cc_final: 0.7555 (ptp)
REVERT: B  362 LYS cc_start: 0.9230 (mttm) cc_final: 0.8740 (mttp)
REVERT: B  401 LYS cc_start: 0.8869 (mttt) cc_final: 0.8609 (pttp)
REVERT: B  417 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8391 (m-30)
REVERT: B  454 TRP cc_start: 0.7805 (m100) cc_final: 0.7321 (m100)
REVERT: B  488 MET cc_start: 0.6846 (mtp) cc_final: 0.6608 (mtp)
  outliers start: 22
  outliers final: 9
  residues processed: 78
  average time/residue: 0.0750
  time to fit residues: 7.5621
Evaluate side-chains
  70 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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 43 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0570
   chunk 31 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 61 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 19 optimal weight:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 40 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    1.3504

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

Flipped N/Q/H residues before XYZ refinement:
A 535 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.096945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.081988 restraints weight = 21853.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.4027 rms_B_bonded: 6.94
r_work (final): 0.4027
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4028
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4028 r_free = 0.4028    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4028 r_free = 0.4028    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4028
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.5262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5233  Z= 0.158
  Angle     :  0.606   7.833   7128  Z= 0.323
  Chirality :  0.046   0.164    755
  Planarity :  0.004   0.044    923
  Dihedral  :  4.672  19.400    704
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 18.32
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.55 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 18.96 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.37 (0.32), residues: 649
  helix: -1.22 (0.58), residues: 76
  sheet: -1.17 (0.37), residues: 181
  loop : -0.63 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 409 
 TYR   0.012   0.002   TYR A 465 
 PHE   0.016   0.002   PHE B 319 
 TRP   0.035   0.002   TRP B 380 
 HIS   0.004   0.001   HIS B 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 5216)
  covalent geometry    : angle       0.60533 ( 7094)
  SS BOND              : bond        0.00180 (   17)
  SS BOND              : angle       0.72762 (   34)
  hydrogen bonds       : bond        0.03822 (  125)
  hydrogen bonds       : angle       6.84750 (  318)

*********************** 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: 20
    poor density    : 68
  time to evaluate  : 0.122 
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: 0.7918 (mt-10) cc_final: 0.7538 (mt-10)
REVERT: A  353 ASN cc_start: 0.8969 (t0) cc_final: 0.8591 (m110)
REVERT: A  537 LYS cc_start: 0.8343 (tptt) cc_final: 0.8011 (tptp)
REVERT: A  604 THR cc_start: 0.6392 (OUTLIER) cc_final: 0.6192 (t)
REVERT: B  188 MET cc_start: 0.7753 (mtt) cc_final: 0.7183 (mmt)
REVERT: B  202 ASP cc_start: 0.8502 (p0) cc_final: 0.7561 (t0)
REVERT: B  320 MET cc_start: 0.8174 (ptp) cc_final: 0.7018 (ptp)
REVERT: B  334 HIS cc_start: 0.8904 (t-90) cc_final: 0.8163 (t-90)
REVERT: B  359 ASP cc_start: 0.9632 (m-30) cc_final: 0.9264 (p0)
REVERT: B  362 LYS cc_start: 0.9228 (mttm) cc_final: 0.8916 (mttm)
REVERT: B  395 GLU cc_start: 0.9221 (tp30) cc_final: 0.8859 (tp30)
REVERT: B  417 ASP cc_start: 0.8972 (OUTLIER) cc_final: 0.8445 (m-30)
REVERT: B  488 MET cc_start: 0.7103 (mtp) cc_final: 0.6878 (mtp)
  outliers start: 20
  outliers final: 12
  residues processed: 82
  average time/residue: 0.0667
  time to fit residues: 7.1631
Evaluate side-chains
  74 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
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  587 ARG
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  273 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  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 46 optimal weight:    0.9980
   chunk 41 optimal weight:    6.9990
   chunk 19 optimal weight:    9.9990
   chunk 8 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 50 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0370
   chunk 55 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.7258

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

Flipped N/Q/H residues before XYZ refinement:
A 364 HIS
** 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 = 0.4362 r_free = 0.4362 target = 0.098506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.083341 restraints weight = 21867.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.4050 rms_B_bonded: 7.04
r_work (final): 0.4050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.5523

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= 0.121
  Angle     :  0.584   7.774   7128  Z= 0.309
  Chirality :  0.045   0.157    755
  Planarity :  0.004   0.040    923
  Dihedral  :  4.631  19.597    704
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.08 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 20.70 %
    Favored  : 76.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.08 (0.32), residues: 649
  helix: -0.39 (0.70), residues: 58
  sheet: -1.12 (0.38), residues: 177
  loop : -0.51 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 409 
 TYR   0.015   0.001   TYR A 414 
 PHE   0.018   0.002   PHE B 311 
 TRP   0.026   0.002   TRP B 269 
 HIS   0.004   0.001   HIS B 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 5216)
  covalent geometry    : angle       0.58398 ( 7094)
  SS BOND              : bond        0.00144 (   17)
  SS BOND              : angle       0.62226 (   34)
  hydrogen bonds       : bond        0.03420 (  125)
  hydrogen bonds       : angle       6.59748 (  318)

*********************** 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: 19
    poor density    : 68
  time to evaluate  : 0.170 
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: 0.7857 (mt-10) cc_final: 0.7489 (mt-10)
REVERT: A  353 ASN cc_start: 0.8894 (t0) cc_final: 0.8495 (m110)
REVERT: A  537 LYS cc_start: 0.8326 (tptt) cc_final: 0.8023 (tptp)
REVERT: A  604 THR cc_start: 0.6411 (OUTLIER) cc_final: 0.6190 (t)
REVERT: A  610 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8672 (pt)
REVERT: B  178 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8803 (tt0)
REVERT: B  188 MET cc_start: 0.7800 (mtt) cc_final: 0.7160 (mmt)
REVERT: B  202 ASP cc_start: 0.8489 (p0) cc_final: 0.7618 (t0)
REVERT: B  210 MET cc_start: 0.7618 (tpp) cc_final: 0.7351 (tpp)
REVERT: B  334 HIS cc_start: 0.8932 (t-90) cc_final: 0.8236 (t-90)
REVERT: B  395 GLU cc_start: 0.9096 (tp30) cc_final: 0.8698 (tp30)
REVERT: B  417 ASP cc_start: 0.8950 (OUTLIER) cc_final: 0.8515 (m-30)
  outliers start: 19
  outliers final: 11
  residues processed: 84
  average time/residue: 0.0695
  time to fit residues: 7.5596
Evaluate side-chains
  74 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  405 ILE
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   chunk 40 optimal weight:    7.9990
   chunk 19 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 52 optimal weight:    0.2980
   chunk 54 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    1.2588

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

Flipped N/Q/H residues before XYZ refinement:
A 364 HIS
** 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 = 0.4320 r_free = 0.4320 target = 0.096057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.080882 restraints weight = 22102.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.4008 rms_B_bonded: 6.97
r_work (final): 0.4008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.5992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5233  Z= 0.148
  Angle     :  0.614   7.027   7128  Z= 0.324
  Chirality :  0.046   0.163    755
  Planarity :  0.004   0.038    923
  Dihedral  :  4.713  20.398    704
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 17.81
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.93 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 22.61 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.17 (0.32), residues: 649
  helix: -0.66 (0.65), residues: 64
  sheet: -1.18 (0.37), residues: 177
  loop : -0.53 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 409 
 TYR   0.014   0.002   TYR A 414 
 PHE   0.016   0.002   PHE B 311 
 TRP   0.030   0.002   TRP B 269 
 HIS   0.005   0.001   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 5216)
  covalent geometry    : angle       0.61355 ( 7094)
  SS BOND              : bond        0.00181 (   17)
  SS BOND              : angle       0.67707 (   34)
  hydrogen bonds       : bond        0.03568 (  125)
  hydrogen bonds       : angle       6.63766 (  318)

*********************** 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
  88 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.134 
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: 0.7909 (mt-10) cc_final: 0.7539 (mt-10)
REVERT: A  353 ASN cc_start: 0.8946 (t0) cc_final: 0.8578 (m110)
REVERT: A  610 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8730 (pt)
REVERT: B  188 MET cc_start: 0.7758 (mtt) cc_final: 0.7205 (mmt)
REVERT: B  202 ASP cc_start: 0.8490 (p0) cc_final: 0.7666 (t0)
REVERT: B  334 HIS cc_start: 0.9076 (t-90) cc_final: 0.8282 (t-90)
REVERT: B  362 LYS cc_start: 0.9196 (mttm) cc_final: 0.8680 (mtmm)
REVERT: B  371 MET cc_start: 0.7015 (ptp) cc_final: 0.6747 (ptp)
REVERT: B  417 ASP cc_start: 0.9043 (OUTLIER) cc_final: 0.8593 (m-30)
  outliers start: 16
  outliers final: 13
  residues processed: 85
  average time/residue: 0.0647
  time to fit residues: 7.1968
Evaluate side-chains
  79 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  213 ASN
Chi-restraints excluded: chain B residue  273 LEU
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  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 24 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0170
   chunk 8 optimal weight:    2.9990
   chunk 13 optimal weight:    9.9990
   chunk 3 optimal weight:    0.7980
   chunk 6 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0270
   chunk 51 optimal weight:    6.9990
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
A 364 HIS
B 146 ASN
** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 487 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.099385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.084248 restraints weight = 21036.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 6.96
r_work (final): 0.4063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.6130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5233  Z= 0.113
  Angle     :  0.622   8.193   7128  Z= 0.322
  Chirality :  0.046   0.163    755
  Planarity :  0.004   0.036    923
  Dihedral  :  4.599  21.827    704
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.54 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 24.52 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.03 (0.32), residues: 649
  helix: -0.28 (0.71), residues: 58
  sheet: -1.07 (0.38), residues: 177
  loop : -0.50 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 409 
 TYR   0.026   0.001   TYR A 414 
 PHE   0.021   0.002   PHE B 311 
 TRP   0.033   0.001   TRP B 269 
 HIS   0.004   0.001   HIS B 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 5216)
  covalent geometry    : angle       0.62210 ( 7094)
  SS BOND              : bond        0.00143 (   17)
  SS BOND              : angle       0.60754 (   34)
  hydrogen bonds       : bond        0.03189 (  125)
  hydrogen bonds       : angle       6.44262 (  318)

*********************** 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
  87 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.217 
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: 0.7831 (mt-10) cc_final: 0.7489 (mt-10)
REVERT: A  353 ASN cc_start: 0.8895 (t0) cc_final: 0.8490 (m110)
REVERT: A  501 TYR cc_start: 0.7589 (OUTLIER) cc_final: 0.6712 (t80)
REVERT: A  604 THR cc_start: 0.6248 (OUTLIER) cc_final: 0.6041 (t)
REVERT: A  610 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8709 (pt)
REVERT: B  188 MET cc_start: 0.7759 (mtt) cc_final: 0.7204 (mmt)
REVERT: B  202 ASP cc_start: 0.8413 (p0) cc_final: 0.7564 (t0)
REVERT: B  210 MET cc_start: 0.7460 (tpp) cc_final: 0.7123 (tpp)
REVERT: B  334 HIS cc_start: 0.9022 (t-90) cc_final: 0.8285 (t-90)
REVERT: B  362 LYS cc_start: 0.9090 (mttm) cc_final: 0.8651 (mtmm)
REVERT: B  371 MET cc_start: 0.6968 (ptp) cc_final: 0.6660 (ptp)
REVERT: B  395 GLU cc_start: 0.9101 (tp30) cc_final: 0.8644 (tp30)
REVERT: B  417 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8548 (m-30)
  outliers start: 17
  outliers final: 13
  residues processed: 84
  average time/residue: 0.0898
  time to fit residues: 9.6329
Evaluate side-chains
  84 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
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  501 TYR
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  273 LEU
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  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 61 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 56 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 45 optimal weight:    0.2980
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 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 = 0.4353 r_free = 0.4353 target = 0.098139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.082940 restraints weight = 21794.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.4034 rms_B_bonded: 7.04
r_work (final): 0.4034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.6354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   5233  Z= 0.141
  Angle     :  0.662  12.137   7128  Z= 0.346
  Chirality :  0.047   0.178    755
  Planarity :  0.004   0.036    923
  Dihedral  :  4.637  20.570    704
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 18.62
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.24 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 23.65 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.33), residues: 649
  helix:  0.36 (0.77), residues: 52
  sheet: -1.12 (0.38), residues: 177
  loop : -0.44 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 464 
 TYR   0.013   0.002   TYR A 465 
 PHE   0.018   0.002   PHE B 311 
 TRP   0.028   0.002   TRP B 269 
 HIS   0.005   0.001   HIS B 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 5216)
  covalent geometry    : angle       0.66158 ( 7094)
  SS BOND              : bond        0.00173 (   17)
  SS BOND              : angle       0.70066 (   34)
  hydrogen bonds       : bond        0.03275 (  125)
  hydrogen bonds       : angle       6.29286 (  318)

*********************** 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
  91 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 70
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7490 (mt-10)
REVERT: A  353 ASN cc_start: 0.8893 (t0) cc_final: 0.8478 (m110)
REVERT: A  501 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.6894 (t80)
REVERT: A  537 LYS cc_start: 0.8309 (tptt) cc_final: 0.8005 (tptp)
REVERT: A  610 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8726 (pt)
REVERT: B  188 MET cc_start: 0.7700 (mtt) cc_final: 0.7137 (mmt)
REVERT: B  202 ASP cc_start: 0.8498 (p0) cc_final: 0.7647 (t0)
REVERT: B  210 MET cc_start: 0.7480 (tpp) cc_final: 0.7069 (tpp)
REVERT: B  334 HIS cc_start: 0.9084 (t-90) cc_final: 0.8254 (t-90)
REVERT: B  362 LYS cc_start: 0.9108 (mttm) cc_final: 0.8665 (mtmm)
REVERT: B  371 MET cc_start: 0.7003 (ptp) cc_final: 0.6691 (ptp)
REVERT: B  417 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8547 (m-30)
  outliers start: 21
  outliers final: 14
  residues processed: 88
  average time/residue: 0.0823
  time to fit residues: 9.5183
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  : 0.212 
-------------------------------------------------------------------------------
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  587 ARG
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  171 VAL
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 63 optimal weight:    0.0980
   chunk 48 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 28 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0980
   chunk 8 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 276 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 = 0.4334 r_free = 0.4334 target = 0.096104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.080332 restraints weight = 21892.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.4036 rms_B_bonded: 7.16
r_work (final): 0.4036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.6608

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= 0.146
  Angle     :  0.715  10.587   7128  Z= 0.360
  Chirality :  0.048   0.253    755
  Planarity :  0.004   0.037    923
  Dihedral  :  4.728  20.598    704
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 19.43
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.24 %
    Favored  : 94.61 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.32), residues: 649
  helix: -0.20 (0.73), residues: 58
  sheet: -1.13 (0.40), residues: 165
  loop : -0.63 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 316 
 TYR   0.020   0.002   TYR B 414 
 PHE   0.033   0.002   PHE A 373 
 TRP   0.032   0.002   TRP B 269 
 HIS   0.004   0.001   HIS B 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 5216)
  covalent geometry    : angle       0.71467 ( 7094)
  SS BOND              : bond        0.00213 (   17)
  SS BOND              : angle       0.74811 (   34)
  hydrogen bonds       : bond        0.03247 (  125)
  hydrogen bonds       : angle       6.10352 (  318)

*********************** 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  : 0.219 
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: 0.7821 (mt-10) cc_final: 0.7443 (mt-10)
REVERT: A  353 ASN cc_start: 0.8966 (t0) cc_final: 0.8556 (m110)
REVERT: A  379 TYR cc_start: 0.8751 (m-80) cc_final: 0.8020 (m-80)
REVERT: A  501 TYR cc_start: 0.7684 (OUTLIER) cc_final: 0.6952 (t80)
REVERT: A  537 LYS cc_start: 0.8304 (tptt) cc_final: 0.8023 (tptp)
REVERT: A  610 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8743 (pt)
REVERT: B  188 MET cc_start: 0.7669 (mtt) cc_final: 0.6577 (mtp)
REVERT: B  202 ASP cc_start: 0.8506 (p0) cc_final: 0.7666 (t0)
REVERT: B  210 MET cc_start: 0.7635 (tpp) cc_final: 0.7178 (tpp)
REVERT: B  276 GLN cc_start: 0.9367 (OUTLIER) cc_final: 0.9140 (tm-30)
REVERT: B  334 HIS cc_start: 0.9055 (t-90) cc_final: 0.8443 (t-90)
REVERT: B  362 LYS cc_start: 0.9137 (mttm) cc_final: 0.8695 (mtmm)
REVERT: B  371 MET cc_start: 0.7027 (ptp) cc_final: 0.6722 (ptp)
REVERT: B  417 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8478 (m-30)
  outliers start: 22
  outliers final: 14
  residues processed: 87
  average time/residue: 0.0792
  time to fit residues: 8.9421
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  : 0.203 
-------------------------------------------------------------------------------
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  587 ARG
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  213 ASN
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  276 GLN
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 21 optimal weight:    0.3980
   chunk 32 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 11 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 12 optimal weight:    0.6980
   chunk 47 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0030
   overall best weight:    0.5590

-------------------------------------------------------------------------------
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 276 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 = 0.4353 r_free = 0.4353 target = 0.097158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.082206 restraints weight = 21778.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.4054 rms_B_bonded: 7.02
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.6664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   5233  Z= 0.127
  Angle     :  0.697  10.234   7128  Z= 0.356
  Chirality :  0.048   0.219    755
  Planarity :  0.004   0.037    923
  Dihedral  :  4.668  19.159    704
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 17.71
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.31 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 25.04 %
    Favored  : 72.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.05 (0.33), residues: 649
  helix: -0.11 (0.73), residues: 58
  sheet: -1.19 (0.39), residues: 169
  loop : -0.51 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 316 
 TYR   0.015   0.001   TYR B 414 
 PHE   0.031   0.002   PHE A 373 
 TRP   0.034   0.002   TRP B 269 
 HIS   0.005   0.001   HIS B 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 5216)
  covalent geometry    : angle       0.69717 ( 7094)
  SS BOND              : bond        0.00181 (   17)
  SS BOND              : angle       0.69314 (   34)
  hydrogen bonds       : bond        0.03046 (  125)
  hydrogen bonds       : angle       5.89713 (  318)

********************** 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
  88 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7443 (mt-10)
REVERT: A  379 TYR cc_start: 0.8692 (m-80) cc_final: 0.7932 (m-80)
REVERT: A  501 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.6886 (t80)
REVERT: A  537 LYS cc_start: 0.8319 (tptt) cc_final: 0.8062 (tptp)
REVERT: A  610 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8752 (pt)
REVERT: B  188 MET cc_start: 0.7688 (mtt) cc_final: 0.6581 (mtp)
REVERT: B  202 ASP cc_start: 0.8379 (p0) cc_final: 0.7573 (t0)
REVERT: B  210 MET cc_start: 0.7692 (tpp) cc_final: 0.7225 (tpp)
REVERT: B  276 GLN cc_start: 0.9339 (OUTLIER) cc_final: 0.9092 (tm-30)
REVERT: B  334 HIS cc_start: 0.9003 (t-90) cc_final: 0.8230 (t-90)
REVERT: B  362 LYS cc_start: 0.9080 (mttm) cc_final: 0.8800 (mptt)
REVERT: B  371 MET cc_start: 0.6969 (ptp) cc_final: 0.6714 (ptp)
REVERT: B  417 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8408 (m-30)
  outliers start: 17
  outliers final: 12
  residues processed: 85
  average time/residue: 0.0754
  time to fit residues: 8.2645
Evaluate side-chains
  84 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  446 ARG
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  276 GLN
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  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 32 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 38 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0970
   chunk 58 optimal weight:   10.0000
   chunk 22 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   chunk 39 optimal weight:    3.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 159 GLN
B 276 GLN
** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.095346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.080595 restraints weight = 22732.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.4014 rms_B_bonded: 7.07
r_work (final): 0.4014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.6870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   5233  Z= 0.148
  Angle     :  0.704  10.506   7128  Z= 0.360
  Chirality :  0.047   0.213    755
  Planarity :  0.004   0.037    923
  Dihedral  :  4.705  18.553    704
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 20.14
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.39 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 25.04 %
    Favored  : 71.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.33), residues: 649
  helix: -0.22 (0.74), residues: 58
  sheet: -1.20 (0.40), residues: 167
  loop : -0.58 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 409 
 TYR   0.017   0.002   TYR B 414 
 PHE   0.029   0.002   PHE A 373 
 TRP   0.030   0.002   TRP B 269 
 HIS   0.006   0.002   HIS B 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 5216)
  covalent geometry    : angle       0.70369 ( 7094)
  SS BOND              : bond        0.00188 (   17)
  SS BOND              : angle       0.71724 (   34)
  hydrogen bonds       : bond        0.03278 (  125)
  hydrogen bonds       : angle       6.00961 (  318)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1488.89 seconds
wall clock time: 26 minutes 18.63 seconds (1578.63 seconds total)