Starting phenix.real_space_refine
on Wed Mar 12 04:35:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wns_37671/03_2025/8wns_37671.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wns_37671/03_2025/8wns_37671.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.42
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wns_37671/03_2025/8wns_37671.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wns_37671/03_2025/8wns_37671.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wns_37671/03_2025/8wns_37671.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wns_37671/03_2025/8wns_37671.cif"
  }
  resolution = 3.42
  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=  -0.001 sd=   0.079
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      32      5.16       5
     C    4710      2.51       5
     N    1189      2.21       5
     O    1295      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7226
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3645
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 468, 3645
          Classifications: {'peptide': 468}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 445}
    Chain: "B"
      Number of atoms: 3525
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 456, 3525
          Classifications: {'peptide': 456}
          Link IDs: {'PTRANS': 23, 'TRANS': 432}
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 4.62, per 1000 atoms: 0.64
  Number of scatterers: 7226
  At special positions: 0
  Unit cell: (103.265, 79.351, 120.657, 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      32     16.00
     O    1295      8.00
     N    1189      7.00
     C    4710      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 211 " - pdb=" SG  CYS B 154 " 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
  Links applied
    NAG-ASN
      " NAG A 701 " - " ASN A 366 "
      " NAG A 702 " - " ASN A 382 "
      " NAG A 703 " - " ASN A 425 "
      " NAG A 704 " - " ASN A 507 "
  Time building additional restraints: 1.86
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1688

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 6 sheets defined
      63.5% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 167 through 175
    Processing helix  chain 'A' and resid 178 through 207
      removed outlier: 3.713A  pdb=" N   THR A 182 " --> pdb=" O   GLY A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 222
      removed outlier: 3.823A  pdb=" N   HIS A 221 " --> pdb=" O   LYS A 218 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   THR A 222 " --> pdb=" O   TRP A 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 218 through 222'
    Processing helix  chain 'A' and resid 230 through 236
      removed outlier: 3.623A  pdb=" N   GLN A 235 " --> pdb=" O   LEU A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 246
    Processing helix  chain 'A' and resid 248 through 256
    Processing helix  chain 'A' and resid 283 through 286
    Processing helix  chain 'A' and resid 287 through 301
    Processing helix  chain 'A' and resid 324 through 342
    Processing helix  chain 'A' and resid 356 through 372
      removed outlier: 3.922A  pdb=" N   PHE A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   SER A 372 " --> pdb=" O   THR A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 394
      removed outlier: 3.848A  pdb=" N   ILE A 389 " --> pdb=" O   ASP A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 407
      No H-bonds generated for 'chain 'A' and resid 405 through 407'
    Processing helix  chain 'A' and resid 412 through 428
    Processing helix  chain 'A' and resid 441 through 445
      removed outlier: 3.568A  pdb=" N   SER A 444 " --> pdb=" O   LEU A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 449
      No H-bonds generated for 'chain 'A' and resid 447 through 449'
    Processing helix  chain 'A' and resid 450 through 461
      removed outlier: 4.087A  pdb=" N   LEU A 456 " --> pdb=" O   ARG A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 534
    Processing helix  chain 'A' and resid 534 through 540
    Processing helix  chain 'A' and resid 585 through 589
      removed outlier: 3.837A  pdb=" N   SER A 589 " --> pdb=" O   ALA A 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 54
    Processing helix  chain 'B' and resid 60 through 70
      removed outlier: 4.209A  pdb=" N   GLY B  64 " --> pdb=" O   ILE B  60 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   HIS B  68 " --> pdb=" O   GLY B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 100
      removed outlier: 3.526A  pdb=" N   ALA B  87 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 114
    Processing helix  chain 'B' and resid 115 through 129
    Processing helix  chain 'B' and resid 129 through 148
    Processing helix  chain 'B' and resid 157 through 179
      removed outlier: 3.683A  pdb=" N   SER B 179 " --> pdb=" O   VAL B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 212
    Processing helix  chain 'B' and resid 218 through 223
    Processing helix  chain 'B' and resid 230 through 242
    Processing helix  chain 'B' and resid 247 through 255
      removed outlier: 4.036A  pdb=" N   LEU B 251 " --> pdb=" O   TRP B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 291
      removed outlier: 3.568A  pdb=" N   ASN B 264 " --> pdb=" O   ASP B 260 " (cutoff:3.500A)
      Proline residue:  B 266  - end of helix
      Proline residue:  B 274  - end of helix
    Processing helix  chain 'B' and resid 292 through 298
    Processing helix  chain 'B' and resid 301 through 311
      removed outlier: 3.596A  pdb=" N   THR B 305 " --> pdb=" O   ALA B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 315
    Processing helix  chain 'B' and resid 316 through 348
      removed outlier: 4.244A  pdb=" N   VAL B 320 " --> pdb=" O   TRP B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 355
    Processing helix  chain 'B' and resid 364 through 380
      removed outlier: 3.560A  pdb=" N   LEU B 368 " --> pdb=" O   PRO B 364 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU B 380 " --> pdb=" O   ALA B 376 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 413
    Processing helix  chain 'B' and resid 424 through 445
    Processing helix  chain 'B' and resid 445 through 458
      removed outlier: 4.450A  pdb=" N   CYS B 449 " --> pdb=" O   GLU B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 467
      removed outlier: 4.029A  pdb=" N   ILE B 462 " --> pdb=" O   THR B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 492
    Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 403
      removed outlier: 6.456A  pdb=" N   LEU A 377 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 7.780A  pdb=" N   THR A 402 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   ALA A 379 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   GLY A 345 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   LEU A 307 " --> pdb=" O   GLY A 345 " (cutoff:3.500A)
      removed outlier: 5.749A  pdb=" N   LEU A 260 " --> pdb=" O   ILE A 306 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   ASP A 308 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   LEU A 262 " --> pdb=" O   ASP A 308 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL A 261 " --> pdb=" O   TYR A 226 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   LEU A 225 " --> pdb=" O   PHE A 467 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267
      removed outlier: 7.024A  pdb=" N   GLN A 280 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 543
      removed outlier: 3.506A  pdb=" N   LEU A 598 " --> pdb=" O   LEU A 624 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 575 through 576
    Processing sheet with id=AA5, first strand: chain 'A' and resid 593 through 594
    Processing sheet with id=AA6, first strand: chain 'B' and resid 357 through 358

    430 hydrogen bonds defined for protein.
    1242 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: 1.88

  Time building geometry restraints manager: 2.19 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: 2251
        1.34 -     1.46: 1758
        1.46 -     1.58: 3354
        1.58 -     1.70: 0
        1.70 -     1.82: 50
  Bond restraints: 7413
  Sorted by residual:
  bond pdb=" N   GLU A 472 "
       pdb=" CA  GLU A 472 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.25e-02 6.40e+03 6.16e+00
  bond pdb=" N   THR A 276 "
       pdb=" CA  THR A 276 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.030 1.29e-02 6.01e+03 5.53e+00
  bond pdb=" N   SER B 315 "
       pdb=" CA  SER B 315 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.25e-02 6.40e+03 5.40e+00
  bond pdb=" N   SER A 536 "
       pdb=" CA  SER A 536 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.23e-02 6.61e+03 5.23e+00
  bond pdb=" CA  SER B 315 "
       pdb=" CB  SER B 315 "
    ideal  model  delta    sigma   weight residual
    1.529  1.494  0.035 1.64e-02 3.72e+03 4.59e+00
  ... (remaining 7408 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 9881
        1.88 -     3.76: 160
        3.76 -     5.64: 34
        5.64 -     7.51: 13
        7.51 -     9.39: 4
  Bond angle restraints: 10092
  Sorted by residual:
  angle pdb=" N   MET B 291 "
        pdb=" CA  MET B 291 "
        pdb=" C   MET B 291 "
      ideal   model   delta    sigma   weight residual
     108.34  113.18   -4.84 1.31e+00 5.83e-01 1.36e+01
  angle pdb=" N   GLY B 382 "
        pdb=" CA  GLY B 382 "
        pdb=" C   GLY B 382 "
      ideal   model   delta    sigma   weight residual
     111.20  115.64   -4.44 1.39e+00 5.18e-01 1.02e+01
  angle pdb=" CB  MET B 227 "
        pdb=" CG  MET B 227 "
        pdb=" SD  MET B 227 "
      ideal   model   delta    sigma   weight residual
     112.70  121.66   -8.96 3.00e+00 1.11e-01 8.92e+00
  angle pdb=" CA  LEU A 307 "
        pdb=" CB  LEU A 307 "
        pdb=" CG  LEU A 307 "
      ideal   model   delta    sigma   weight residual
     116.30  125.69   -9.39 3.50e+00 8.16e-02 7.20e+00
  angle pdb=" CA  LEU B 117 "
        pdb=" CB  LEU B 117 "
        pdb=" CG  LEU B 117 "
      ideal   model   delta    sigma   weight residual
     116.30  125.30   -9.00 3.50e+00 8.16e-02 6.61e+00
  ... (remaining 10087 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 3720
       17.53 -    35.06: 493
       35.06 -    52.59: 126
       52.59 -    70.12: 26
       70.12 -    87.66: 5
  Dihedral angle restraints: 4370
    sinusoidal: 1734
      harmonic: 2636
  Sorted by residual:
  dihedral pdb=" CB  CYS A 211 "
           pdb=" SG  CYS A 211 "
           pdb=" SG  CYS B 154 "
           pdb=" CB  CYS B 154 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -145.51   59.51     1      1.00e+01 1.00e-02 4.73e+01
  dihedral pdb=" CA  GLU B 257 "
           pdb=" C   GLU B 257 "
           pdb=" N   MET B 258 "
           pdb=" CA  MET B 258 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.01   18.99     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CG  ARG B 360 "
           pdb=" CD  ARG B 360 "
           pdb=" NE  ARG B 360 "
           pdb=" CZ  ARG B 360 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.29  -44.29     2      1.50e+01 4.44e-03 1.04e+01
  ... (remaining 4367 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 865
       0.040 -    0.081: 227
       0.081 -    0.121: 65
       0.121 -    0.162: 5
       0.162 -    0.202: 3
  Chirality restraints: 1165
  Sorted by residual:
  chirality pdb=" C1  NAG A 704 "
            pdb=" ND2 ASN A 507 "
            pdb=" C2  NAG A 704 "
            pdb=" O5  NAG A 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.20   -0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" C1  NAG A 702 "
            pdb=" ND2 ASN A 382 "
            pdb=" C2  NAG A 702 "
            pdb=" O5  NAG A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.23   -0.17 2.00e-01 2.50e+01 7.51e-01
  chirality pdb=" CG  LEU A 339 "
            pdb=" CB  LEU A 339 "
            pdb=" CD1 LEU A 339 "
            pdb=" CD2 LEU A 339 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.56e-01
  ... (remaining 1162 not shown)

  Planarity restraints: 1261
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 469 "   -0.017 2.00e-02 2.50e+03   1.39e-02 4.85e+00
        pdb=" CG  TRP B 469 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 469 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 469 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 469 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 469 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 469 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 469 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 469 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 469 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 337 "    0.013 2.00e-02 2.50e+03   1.43e-02 4.11e+00
        pdb=" CG  TYR B 337 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 337 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 337 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 337 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 337 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 337 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B 337 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 350 "    0.028 5.00e-02 4.00e+02   4.32e-02 2.98e+00
        pdb=" N   PRO B 351 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B 351 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 351 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1258 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 814
        2.75 -     3.28: 7218
        3.28 -     3.82: 12320
        3.82 -     4.36: 13302
        4.36 -     4.90: 23556
  Nonbonded interactions: 57210
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 463 "
            pdb=" NH2 ARG A 531 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" O   LYS A 417 "
            pdb=" OG1 THR A 421 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   HIS A 266 "
            pdb=" OH  TYR A 313 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   SER A 582 "
            pdb=" OG  SER A 582 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" NH1 ARG A 535 "
            pdb=" OD1 ASN B 153 "
     model   vdw
     2.259 3.120
  ... (remaining 57205 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=1.00 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:             1.190
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     19.830
  Find NCS groups from input model:        0.100
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
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   0.037   7413  Z= 0.213
  Angle     :  0.646   9.392  10092  Z= 0.311
  Chirality :  0.040   0.202   1165
  Planarity :  0.004   0.043   1257
  Dihedral  : 16.657  87.656   2679
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 30.06 %
    Favored  : 69.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.29 (0.28), residues: 920
  helix:  1.76 (0.22), residues: 547
  sheet:  0.80 (0.78), residues: 57
  loop : -0.75 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.001   TRP B 469 
 HIS   0.004   0.001   HIS B  68 
 PHE   0.015   0.001   PHE A 542 
 TYR   0.033   0.001   TYR B 337 
 ARG   0.002   0.000   ARG A 183 

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 104
  time to evaluate  : 0.852 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 106
  average time/residue: 0.1433
  time to fit residues: 23.1365
Evaluate side-chains
  104 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 102
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  536 SER
Chi-restraints excluded: chain B residue   81 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 71 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 82 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 358 HIS ** 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 = 0.4384 r_free = 0.4384 target = 0.188606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.130472 restraints weight = 10371.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 3.83
r_work: 0.3387 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.0839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7413  Z= 0.202
  Angle     :  0.607   7.978  10092  Z= 0.292
  Chirality :  0.040   0.200   1165
  Planarity :  0.004   0.042   1257
  Dihedral  :  4.349  55.860   1073
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 25.94 %
    Favored  : 70.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.57 (0.28), residues: 920
  helix:  2.09 (0.22), residues: 539
  sheet:  0.45 (0.72), residues: 62
  loop : -0.69 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 469 
 HIS   0.002   0.001   HIS A 557 
 PHE   0.021   0.001   PHE B 442 
 TYR   0.020   0.001   TYR B 337 
 ARG   0.003   0.000   ARG A 452 

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 110
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 ASN cc_start: 0.8352 (t0) cc_final: 0.7810 (t0)
REVERT: A  339 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6511 (mm)
REVERT: A  360 PHE cc_start: 0.7872 (m-80) cc_final: 0.7528 (m-80)
REVERT: B  145 TYR cc_start: 0.8556 (m-80) cc_final: 0.7923 (m-80)
  outliers start: 27
  outliers final: 14
  residues processed: 129
  average time/residue: 0.1502
  time to fit residues: 28.1807
Evaluate side-chains
  117 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  396 ASN
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain B residue   93 TYR
Chi-restraints excluded: chain B residue  240 GLN
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  394 ILE
Chi-restraints excluded: chain B residue  407 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 82 optimal weight:    2.9990
   chunk 76 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 86 optimal weight:    6.9990
   chunk 77 optimal weight:    7.9990
   chunk 9 optimal weight:    0.2980
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 620 HIS
** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.187358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.121918 restraints weight = 10463.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 3.83
r_work: 0.3371 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.1150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7413  Z= 0.235
  Angle     :  0.583   7.541  10092  Z= 0.285
  Chirality :  0.040   0.176   1165
  Planarity :  0.004   0.044   1257
  Dihedral  :  3.931  16.884   1070
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 26.97 %
    Favored  : 69.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.56 (0.28), residues: 920
  helix:  2.13 (0.22), residues: 539
  sheet:  0.39 (0.73), residues: 62
  loop : -0.77 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 469 
 HIS   0.003   0.001   HIS A 557 
 PHE   0.016   0.001   PHE A 542 
 TYR   0.016   0.002   TYR B 337 
 ARG   0.006   0.000   ARG A 207 

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 ASN cc_start: 0.8358 (t0) cc_final: 0.7779 (t0)
REVERT: A  339 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6461 (mm)
REVERT: A  360 PHE cc_start: 0.7876 (m-80) cc_final: 0.7563 (m-80)
REVERT: B   92 CYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8453 (t)
REVERT: B  145 TYR cc_start: 0.8672 (m-80) cc_final: 0.7938 (m-80)
REVERT: B  442 PHE cc_start: 0.7959 (m-80) cc_final: 0.7673 (m-80)
  outliers start: 25
  outliers final: 12
  residues processed: 128
  average time/residue: 0.1467
  time to fit residues: 27.6035
Evaluate side-chains
  116 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  396 ASN
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  543 HIS
Chi-restraints excluded: chain B residue   92 CYS
Chi-restraints excluded: chain B residue  240 GLN
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  394 ILE
Chi-restraints excluded: chain B residue  407 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 67 optimal weight:    0.8980
   chunk 42 optimal weight:    0.4980
   chunk 3 optimal weight:    4.9990
   chunk 81 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 89 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 233 HIS
** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 485 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.197628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.152397 restraints weight = 10625.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.4019 rms_B_bonded: 3.52
r_work: 0.3598 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.1345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7413  Z= 0.205
  Angle     :  0.581   7.314  10092  Z= 0.280
  Chirality :  0.040   0.172   1165
  Planarity :  0.004   0.046   1257
  Dihedral  :  3.861  17.247   1070
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 25.16 %
    Favored  : 70.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.58 (0.28), residues: 920
  helix:  2.15 (0.22), residues: 539
  sheet:  0.36 (0.73), residues: 62
  loop : -0.76 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 469 
 HIS   0.009   0.001   HIS B 485 
 PHE   0.016   0.001   PHE A 542 
 TYR   0.031   0.002   TYR B 337 
 ARG   0.004   0.000   ARG A 207 

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 118
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 ASN cc_start: 0.8234 (t0) cc_final: 0.7805 (t0)
REVERT: A  339 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6587 (mm)
REVERT: A  360 PHE cc_start: 0.7904 (m-80) cc_final: 0.7539 (m-80)
REVERT: B   92 CYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8372 (t)
REVERT: B  145 TYR cc_start: 0.8779 (m-80) cc_final: 0.8094 (m-80)
REVERT: B  442 PHE cc_start: 0.7607 (m-80) cc_final: 0.7307 (m-80)
REVERT: B  495 TYR cc_start: 0.7484 (t80) cc_final: 0.7173 (t80)
  outliers start: 35
  outliers final: 15
  residues processed: 144
  average time/residue: 0.1834
  time to fit residues: 39.7385
Evaluate side-chains
  122 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 1.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  396 ASN
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  543 HIS
Chi-restraints excluded: chain B residue   92 CYS
Chi-restraints excluded: chain B residue   93 TYR
Chi-restraints excluded: chain B residue  240 GLN
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  394 ILE
Chi-restraints excluded: chain B residue  437 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0370
   chunk 21 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 GLN
** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 485 HIS
** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.193841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.130063 restraints weight = 10345.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 4.24
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.1493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7413  Z= 0.191
  Angle     :  0.583   7.874  10092  Z= 0.281
  Chirality :  0.039   0.168   1165
  Planarity :  0.004   0.047   1257
  Dihedral  :  3.897  19.238   1070
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 25.94 %
    Favored  : 69.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.58 (0.28), residues: 920
  helix:  2.19 (0.22), residues: 534
  sheet:  0.34 (0.73), residues: 62
  loop : -0.78 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 469 
 HIS   0.011   0.001   HIS B 485 
 PHE   0.016   0.001   PHE A 542 
 TYR   0.021   0.001   TYR B 337 
 ARG   0.006   0.000   ARG A 207 

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 110
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 ASN cc_start: 0.8354 (t0) cc_final: 0.7912 (t0)
REVERT: A  339 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6522 (mm)
REVERT: A  360 PHE cc_start: 0.7905 (m-80) cc_final: 0.7529 (m-80)
REVERT: B   92 CYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8520 (t)
REVERT: B  128 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8769 (mm)
REVERT: B  145 TYR cc_start: 0.8494 (m-80) cc_final: 0.7789 (m-80)
REVERT: B  442 PHE cc_start: 0.7861 (m-80) cc_final: 0.7610 (m-80)
REVERT: B  447 MET cc_start: 0.6473 (tpp) cc_final: 0.5804 (tpp)
REVERT: B  495 TYR cc_start: 0.7556 (t80) cc_final: 0.7226 (t80)
  outliers start: 32
  outliers final: 19
  residues processed: 135
  average time/residue: 0.1355
  time to fit residues: 27.6696
Evaluate side-chains
  123 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  396 ASN
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  543 HIS
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   92 CYS
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  394 ILE
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  425 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 57 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 84 optimal weight:    0.0970
   chunk 6 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 10 optimal weight:    0.4980
   chunk 3 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 213 HIS
B 284 ASN
** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.191941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.133630 restraints weight = 10396.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3787 rms_B_bonded: 3.57
r_work: 0.3455 rms_B_bonded: 4.59 restraints_weight: 0.5000
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7413  Z= 0.190
  Angle     :  0.594   8.861  10092  Z= 0.286
  Chirality :  0.040   0.206   1165
  Planarity :  0.004   0.046   1257
  Dihedral  :  4.062  40.194   1070
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 25.55 %
    Favored  : 69.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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:  1.63 (0.28), residues: 920
  helix:  2.24 (0.23), residues: 534
  sheet:  0.33 (0.74), residues: 62
  loop : -0.77 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 469 
 HIS   0.003   0.001   HIS B  68 
 PHE   0.020   0.001   PHE A 337 
 TYR   0.038   0.002   TYR B 337 
 ARG   0.005   0.000   ARG A 207 

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 107
  time to evaluate  : 1.661 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 ASN cc_start: 0.8288 (t0) cc_final: 0.7858 (t0)
REVERT: A  339 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6393 (mm)
REVERT: A  360 PHE cc_start: 0.7847 (m-80) cc_final: 0.7535 (m-80)
REVERT: B   92 CYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8324 (t)
REVERT: B  145 TYR cc_start: 0.8748 (m-80) cc_final: 0.8124 (m-80)
REVERT: B  258 MET cc_start: 0.5642 (pmm) cc_final: 0.5218 (pmm)
REVERT: B  281 THR cc_start: 0.8598 (m) cc_final: 0.8256 (p)
REVERT: B  442 PHE cc_start: 0.7966 (m-80) cc_final: 0.7655 (m-80)
REVERT: B  495 TYR cc_start: 0.7541 (t80) cc_final: 0.7282 (t80)
  outliers start: 35
  outliers final: 22
  residues processed: 136
  average time/residue: 0.2052
  time to fit residues: 42.1670
Evaluate side-chains
  125 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  396 ASN
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  543 HIS
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   92 CYS
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  154 CYS
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  341 CYS
Chi-restraints excluded: chain B residue  394 ILE
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  486 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 53 optimal weight:    7.9990
   chunk 19 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 76 optimal weight:    9.9990
   chunk 84 optimal weight:    4.9990
   chunk 32 optimal weight:    0.7980
   chunk 42 optimal weight:    7.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 294 GLN
** B 358 HIS ** 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 = 0.4374 r_free = 0.4374 target = 0.186260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.126241 restraints weight = 10490.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 3.80
r_work: 0.3376 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050   7413  Z= 0.428
  Angle     :  0.719   8.636  10092  Z= 0.350
  Chirality :  0.044   0.184   1165
  Planarity :  0.004   0.048   1257
  Dihedral  :  4.474  35.539   1070
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 25.55 %
    Favored  : 69.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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:  1.33 (0.28), residues: 920
  helix:  2.04 (0.22), residues: 539
  sheet:  0.02 (0.71), residues: 65
  loop : -1.00 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 469 
 HIS   0.007   0.001   HIS A 557 
 PHE   0.030   0.002   PHE A 524 
 TYR   0.028   0.002   TYR B 337 
 ARG   0.005   0.001   ARG A 604 

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 101
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 ASN cc_start: 0.8373 (t0) cc_final: 0.7918 (t0)
REVERT: A  339 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.6892 (mm)
REVERT: B  189 MET cc_start: 0.8631 (tmm) cc_final: 0.8429 (tmm)
REVERT: B  258 MET cc_start: 0.6113 (pmm) cc_final: 0.5812 (pmm)
REVERT: B  431 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8555 (pp)
REVERT: B  442 PHE cc_start: 0.8032 (m-80) cc_final: 0.7694 (m-80)
  outliers start: 36
  outliers final: 26
  residues processed: 126
  average time/residue: 0.1761
  time to fit residues: 32.8317
Evaluate side-chains
  122 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 94
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  396 ASN
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  403 SER
Chi-restraints excluded: chain A residue  429 ASN
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  542 PHE
Chi-restraints excluded: chain A residue  543 HIS
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   93 TYR
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  240 GLN
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  394 ILE
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  437 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 77 optimal weight:    8.9990
   chunk 11 optimal weight:    6.9990
   chunk 55 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 33 optimal weight:    0.0030
   chunk 44 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 66 optimal weight:    0.7980
   chunk 61 optimal weight:    4.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.5790

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 358 HIS ** 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 = 0.4415 r_free = 0.4415 target = 0.190652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.124918 restraints weight = 10504.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 3.77
r_work: 0.3408 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7413  Z= 0.192
  Angle     :  0.631   9.034  10092  Z= 0.300
  Chirality :  0.041   0.190   1165
  Planarity :  0.004   0.046   1257
  Dihedral  :  4.120  29.152   1070
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 27.48 %
    Favored  : 69.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.54 (0.28), residues: 920
  helix:  2.20 (0.22), residues: 538
  sheet:  0.21 (0.73), residues: 62
  loop : -0.91 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 469 
 HIS   0.003   0.001   HIS B  68 
 PHE   0.017   0.001   PHE B 327 
 TYR   0.044   0.002   TYR B 337 
 ARG   0.004   0.000   ARG A 207 

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 103
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 ASN cc_start: 0.8383 (t0) cc_final: 0.7950 (t0)
REVERT: A  339 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6486 (mm)
REVERT: A  360 PHE cc_start: 0.7909 (m-80) cc_final: 0.7563 (m-80)
REVERT: A  575 LEU cc_start: 0.7870 (mp) cc_final: 0.7631 (mp)
REVERT: B  170 MET cc_start: 0.7891 (mtt) cc_final: 0.7621 (mtm)
REVERT: B  258 MET cc_start: 0.6102 (pmm) cc_final: 0.5872 (pmm)
REVERT: B  281 THR cc_start: 0.8550 (m) cc_final: 0.8195 (p)
REVERT: B  442 PHE cc_start: 0.7884 (m-80) cc_final: 0.7568 (m-80)
  outliers start: 25
  outliers final: 17
  residues processed: 125
  average time/residue: 0.1356
  time to fit residues: 25.7367
Evaluate side-chains
  119 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  396 ASN
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  543 HIS
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  154 CYS
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  341 CYS
Chi-restraints excluded: chain B residue  394 ILE
Chi-restraints excluded: chain B residue  477 HIS
Chi-restraints excluded: chain B residue  486 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 49 optimal weight:    8.9990
   chunk 77 optimal weight:    9.9990
   chunk 78 optimal weight:    0.9990
   chunk 89 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 52 optimal weight:    7.9990
   chunk 4 optimal weight:    0.0670
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.7322

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 358 HIS ** 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 = 0.4421 r_free = 0.4421 target = 0.191062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.127245 restraints weight = 10574.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 3.98
r_work: 0.3390 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7413  Z= 0.207
  Angle     :  0.634   9.969  10092  Z= 0.299
  Chirality :  0.041   0.179   1165
  Planarity :  0.004   0.046   1257
  Dihedral  :  4.027  25.975   1070
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 27.48 %
    Favored  : 69.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.53 (0.29), residues: 920
  helix:  2.22 (0.23), residues: 538
  sheet:  0.16 (0.73), residues: 62
  loop : -0.93 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 469 
 HIS   0.003   0.001   HIS B  68 
 PHE   0.016   0.001   PHE B 327 
 TYR   0.020   0.002   TYR B 337 
 ARG   0.004   0.000   ARG A 207 

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 ASN cc_start: 0.8359 (t0) cc_final: 0.7944 (t0)
REVERT: A  339 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6401 (mm)
REVERT: A  360 PHE cc_start: 0.7864 (m-80) cc_final: 0.7547 (m-80)
REVERT: A  575 LEU cc_start: 0.7865 (mp) cc_final: 0.7629 (mp)
REVERT: B  154 CYS cc_start: 0.6216 (OUTLIER) cc_final: 0.5353 (m)
REVERT: B  170 MET cc_start: 0.7933 (mtt) cc_final: 0.7613 (mtm)
REVERT: B  258 MET cc_start: 0.6151 (pmm) cc_final: 0.5938 (pmm)
REVERT: B  281 THR cc_start: 0.8505 (m) cc_final: 0.8156 (p)
REVERT: B  442 PHE cc_start: 0.7858 (m-80) cc_final: 0.7563 (m-80)
REVERT: B  447 MET cc_start: 0.6603 (tpp) cc_final: 0.5928 (tpp)
  outliers start: 23
  outliers final: 16
  residues processed: 125
  average time/residue: 0.2313
  time to fit residues: 44.0461
Evaluate side-chains
  119 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  396 ASN
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  543 HIS
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  154 CYS
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  394 ILE
Chi-restraints excluded: chain B residue  477 HIS
Chi-restraints excluded: chain B residue  486 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 34 optimal weight:    0.0770
   chunk 6 optimal weight:    0.6980
   chunk 0 optimal weight:   40.0000
   chunk 81 optimal weight:    0.9980
   chunk 84 optimal weight:    0.0070
   chunk 3 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   overall best weight:    0.4156

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 358 HIS ** 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 = 0.4437 r_free = 0.4437 target = 0.193067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.128156 restraints weight = 10592.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 3.92
r_work: 0.3474 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7413  Z= 0.173
  Angle     :  0.622  10.674  10092  Z= 0.290
  Chirality :  0.040   0.165   1165
  Planarity :  0.004   0.044   1257
  Dihedral  :  3.888  23.842   1070
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 27.48 %
    Favored  : 69.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.58 (0.29), residues: 920
  helix:  2.25 (0.23), residues: 539
  sheet:  0.30 (0.73), residues: 62
  loop : -0.95 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP B 469 
 HIS   0.003   0.001   HIS B  68 
 PHE   0.015   0.001   PHE A 542 
 TYR   0.015   0.001   TYR B 109 
 ARG   0.004   0.000   ARG A 207 

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 1.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 ASN cc_start: 0.8300 (t0) cc_final: 0.7877 (t0)
REVERT: A  339 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6291 (mm)
REVERT: A  360 PHE cc_start: 0.7914 (m-80) cc_final: 0.7604 (m-80)
REVERT: A  575 LEU cc_start: 0.7833 (mp) cc_final: 0.7499 (mp)
REVERT: B   43 LEU cc_start: 0.8186 (mm) cc_final: 0.7652 (tt)
REVERT: B   68 HIS cc_start: 0.8392 (OUTLIER) cc_final: 0.8157 (m170)
REVERT: B  154 CYS cc_start: 0.6023 (OUTLIER) cc_final: 0.5244 (m)
REVERT: B  170 MET cc_start: 0.7856 (mtt) cc_final: 0.7593 (mtm)
REVERT: B  263 LYS cc_start: 0.8290 (mmmt) cc_final: 0.8012 (tppt)
REVERT: B  281 THR cc_start: 0.8546 (m) cc_final: 0.8205 (p)
REVERT: B  447 MET cc_start: 0.6640 (tpp) cc_final: 0.5956 (tpp)
REVERT: B  495 TYR cc_start: 0.7794 (t80) cc_final: 0.7523 (t80)
  outliers start: 23
  outliers final: 17
  residues processed: 128
  average time/residue: 0.2067
  time to fit residues: 40.5397
Evaluate side-chains
  119 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 1.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  396 ASN
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  543 HIS
Chi-restraints excluded: chain B residue   68 HIS
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  154 CYS
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  341 CYS
Chi-restraints excluded: chain B residue  394 ILE
Chi-restraints excluded: chain B residue  477 HIS
Chi-restraints excluded: chain B residue  486 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 63 optimal weight:    7.9990
   chunk 84 optimal weight:    0.0010
   chunk 11 optimal weight:    5.9990
   chunk 52 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 90 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 82 optimal weight:    0.6980
   chunk 67 optimal weight:    7.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.8388

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 358 HIS ** 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 = 0.4490 r_free = 0.4490 target = 0.197149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.132262 restraints weight = 10363.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3745 rms_B_bonded: 3.23
r_work: 0.3521 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7413  Z= 0.223
  Angle     :  0.639  10.786  10092  Z= 0.302
  Chirality :  0.041   0.164   1165
  Planarity :  0.004   0.045   1257
  Dihedral  :  3.926  22.889   1070
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 27.87 %
    Favored  : 68.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.52 (0.29), residues: 920
  helix:  2.24 (0.23), residues: 539
  sheet:  0.17 (0.73), residues: 62
  loop : -1.02 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP B 469 
 HIS   0.003   0.001   HIS A 557 
 PHE   0.020   0.001   PHE B 327 
 TYR   0.015   0.002   TYR B 109 
 ARG   0.004   0.000   ARG A 207 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4653.47 seconds
wall clock time: 84 minutes 33.08 seconds (5073.08 seconds total)